The Astros going into 2020 are right now over the Competitive Balance Tax threshold (as most serious contenders should be), which would make them a tax payor for the first time. Owners treat the CBT as a more imposing boundary than they should, and Crane can easily play that game if he wants. Circling back to the draft and young talent situation noted above, teams of course covet players in their cost-controlled years because they can get so much surplus value out of them. The Astros are no different and in some ways are the modern standard-bearer for it.
As the story goes, the Astros under Luhnow as GM undertook a complete razing of the organization — one that saw them lose more than 300 games across three seasons and run a derelict payroll of million at one point — in the service of a better tomorrow. They landed on talents like Carlos Correa and Alex Bregman and Lance McCullers Jr. and paired them with star-level holdovers from prior regimes like Altuve, George Springer, and Dallas Keuchel. Along the way they tapped into their young talent base in order to swing trades for Ken Giles and Justin Verlander. Not 10 weeks after hoisting the trophy, they executed a blockbuster swap for Gerrit Cole and swiftly turned him into the most dominant starting pitcher in baseball. Then came the most recent deadline addition of Zack Greinke, whose presence in the playoff rotation reinforced those assumptions noted above. Supposing that one or more additional titles would follow seemed less of a reach than it normally does in this sport of ours. 
As part of MLB commissioner Rob Manfred’s ruling, the Astros will lose their first- and second-round draft picks in both 2020 and 2021. The Astros still have some high-ceiling prospects and “sophomores” in the fold, but promotions and trades in tandem with lower picks (a function of their recent success) have thinned that particular herd. Also, don’t forget that the current structure of the First-Year Player Draft is such that it’s more than “just” the loss of high picks. Losing picks also entails losing money in the signing bonus pool, and the effects of that cascade throughout the entire draft class. Losing your top two picks necessarily entails losing the biggest parts of those pools. It’s too much to say that the Astros’ next two drafts are squandered, but the likely future value of picks drops steeply and in a non-linear fashion the deeper you go.  
When Corey Seager grounded out to Jose Altuve for the final out of the 2017 World Series, the assumption was that it wouldn’t be the last time this Astros core ended the season in a pile on the mound. Assumptions are especially perilous in a sport like baseball — so often a loyal subject to randomness — but the Jeff Luhnow Astros seemed bound for dynasty-hood. 

The Astros will feel the loss of draft picks

Going forward, though, do we really know how good the Astros’ hitters are? Highly regarded batsmen like Altuve, Springer, Correa, and Bregman are surely productive in any context and in the absence of nefarious aids, but how productive? Data say the cheating worked, and it follows that Houston hitters must cope with some decline, or at least a lower baseline, now that they’ve (presumably) been dragged back into compliance. That, then, affects their ceiling and outlook in future seasons. We mostly know what this team is, which is a good one, but we don’t fully know what this team is because of the rule-breaking.

Crane may now be even less inclined to invest

“Forget the more stable statistics underlying plate discipline: this also manifested as a big spike in their team triple-slash line. As a unit, the Houston offense ranked first in the league in 2017, with a .282/.340/.478 slash line. Each number was the best in all of baseball. In March and April, however–the only months without any sign of a competent signal interception scheme–they batted a “lowly” .272/.340/.425 (second in average, third in on-base, and eighth in slugging). It’s not that they were terrible without advance knowledge of the incoming pitch, but they also didn’t quite play like the Murderer’s Row they came to resemble over the rest of the season.”
Dealing both of them lowers Crane’s costs and pays that fine while also adding cheap young players to the system. At the same time, it would significantly reduce Houston’s chances of winning it all in 2020. How Crane structures the post-sanctions team could be the single biggest factor in all of this. 
The Astros came up short in 2018, and in 2019 a Howie Kendrick home run — one of the clutchest in World Series history — ripped a second title from Houston’s grasp. You know what happened next. MLB‘s investigation into Houston’s electronic sign-stealing yielded tough penalties, owner Jim Crane fired Luhnow and manager A.J. Hinch, and the club’s reputation was further sullied Monday afternoon. 
So what will become of the Astros once the games that count start being played? There’s no way to answer that question for any team, least of all one with as many uncertainties as Houston. They’ll at least be good, but beyond that the possibilities range from missing the playoffs with a win total in the 80s to once again topping 100 victories and getting that second title. How those factors above play out will determine where the Astros land on that continuum in 2020 and beyond. Whatever the specifics, the expectation now is that the Astros won’t be a dynasty and may not even be thought of as one if they do win it all again. That’s not how things were back when Altuve made that final play on Nov. 1, 2017. Things, though, have changed in ways we couldn’t have imagined back then.  Manfred also fined the Astros million, the maximum allowable amount. While that shouldn’t be enough to matter to man of Crane’s means and a franchise of the Astros’ resources, it probably will. We’re in an era in which teams seem to seek out reasons and incentives not to invest in player payroll. Sometimes this is nothing more than creative lying about the financials, which teams as privately held entities are under no obligation to disclose. Give a club the cover of a million expense for which they did not budget, and you’ve got an excuse that’s strong by the usual standards. 

The cheating made a difference

While it says here that front office decision makers are generally overvalued right now — there’s too much uniformity from club to club, and the real differences lie in ownership’s willingness to spend — there’s no doubting the effectiveness of Luhnow’s approach, at least in the raw terms of recent wins and losses. There’s also no doubting Hinch’s effectiveness in implementing that approach on the field. 

So how do you get more of those when your system is starting to dry up and the draft figures to provide little help over the next two years? You trade away team-controlled players. Springer is headed to arbitration, and his salary as a third-year arbitration-eligible player could be the difference in the Astros’ paying the luxury tax or not. Throw in the fact that the Astros and Springer are million apart — coincidentally the same amount as that fine levied against Houston — and the stakes are notable. Springer was the subject of trade rumors even before Manfred’s ruling, and that ruling has perhaps made it more likely that Springer will be traded. Correa trade speculation has also been bandied about. He’ll be owed million for 2020, and because of that lower price tag and the extra year of team control relative Springer he could net the Astros a higher return in trade. 

The Astros will very likely still be a very good team in 2020, and will in most quarters be the favorites in the tough AL West. No matter the damage to the brand, the Astros’ winning the 2020 World Series is a plausible outcome. The scandal and its consequences, however, have put a deep layer of uncertainty on top of the Astros and their near-, mid-, and long-term outlooks. For a number of reasons — all self-inflicted — it’s hard to know what to make of Houston going forward.
Crane also has rarely invested in the product at a level befitting their recent status as World Series favorites. Just twice on Crane’s watch have they ended the season with a top-10 payroll, and their Opening Day payroll prior to last season actually went down. Bear in mind that Forbes estimated the 2013 Astros to be the most profitable team in MLB history. Like most other owners, Crane has made de rigueur invocations of financial limitations in the face of all evidence and even suggested that his Astros aren’t a big-revenue club. The population and media market rankings of the Houston metropolitan area of course suggest otherwise. 

There’s been some brain drain

(Do yourself a favor and read Arthur’s writings on this matter.) As well, Joe Sheehan in his excellent subscription newsletter researched fastball counts as a reasonable proxy for what the Astros were doing — i.e., spitting on offspeed stuff until they knew a fastball was in the immediate offing — and not surprisingly found that such knowledge makes a huge difference. On another level, the Astros were found to have used the cheating system throughout the 2017 postseason. While it’s probably a bridge a bit too far, one could if he or she wanted discount those October accomplishments on that basis. That’s perhaps too provocative of an approach, but any discussion of a dynasty is rendered moot if that first title is rendered dubious.  When it comes to replacing Luhnow on a permanent basis, there will be quite a bit of pressure to bring in someone from outside the organization. Manfred, after all, directly criticized the baseball operations “culture” in Houston. Hiring externally is probably the right thing to do, but it may not be the route Crane takes. Even if he does tab one of Luhnow’s lieutenants as the next permanent GM, something imprecise figures to be lost. There’s no measuring how the loss of GM and manager will affect Houston on the field in the seasons to come, but the most reasonable guess is that it will cost them in some way. Crane was right to fire Luhnow and Hinch, but it has some bearing on how the team fares. 

Even though some Astros players told investigators that they didn’t believe the sign-stealing scheme made much of a difference, the numbers say otherwise. Over at Baseball Prospectus, Rob Arthur researched the issue by combing through game audio to determine the parameters of the tell-tale banging. He found that within those parameters, the Astros drastically improved in terms of plate discipline. He also found this: