The Astros finished with the worst record in franchise history. When you lose more then 100 games there is going to be a lot of facets of the game where you are weak. I know you are going to be shocked to hear that the Astros were not a good fielding team last season. In point of fact, they haven't been a good fielding team in quite some time.
One of the hallmarks of a lack of analysis is the lack of success in nearly every facet of the game. The Astros don't get on base, they don't hit for power, outside of Michael Bourn they didn't run the bases and they don't support their pitchers. As you might imagine, matching young pitchers with bad fielding has disastrous results.
DER: .680 (28th)
RA: 796 (28th)
FLD%: .981 (25th)
Baseball Reference: +24 runs (8th)
Fangraphs: -16.6 runs (23rd)
Fielding Bible: -14 runs (22nd)
Baseball Prospectus: -5.7 (21st)
Composite Runs: -3.1
The four fielding systems are actually quite kind to the Astros given their DER. Even their fielding percentage looks worse than the individual fielding numbers. Of course, we trust the four experts a lot more than fielding percentage. Still, they rate as clearly below average, according to what we see here.
Furthermore, trading away Michael Bourn and Hunter Pence would seemingly hurt in this regard, but their individual numbers were shaky at best last season. That isn't to say they were shaky fielders. But with hitting, fielders can have a slump or years where things just don't go as planned.
Clint Barmes was the odd-man-out in Colorado. Funny, but if the Rockies had known this, they would have put him at second base and forgotten about Mark Ellis and Jose Lopez. Shortstop is his best natural position and he showed it last season. Alex Gonzalez and Barmes are neck and neck for the title of best defensive shortstop last season, but neither will win the award.
Chris Johnson had a horrible year for the ages. His batting average on balls in play plummeted to normal levels and therefore his value dropped as well. Defensively, Johnson has Mark Reynolds to thank for not being the worst third baseman in baseball. As it stands, he was the worst in the National League, and that is saying something considering he lost his job over the last two months.
As you might imagine, a last-place team is always in a state of flux. Jason Castro will be the catcher if his knees hold up. Carlos Lee should be at first base, but Brett Wallace has a chance as well. Jose Altuve should be the second baseman, but he could be bumped if he struggles. Clint Barmes is a free agent, and third base is a three-way competition. We haven't even gotten to the outfield yet. I think you're getting the idea.
What we can say in favor of these current Astros is that they will have a lot of competition for a lot of spots. That's a good thing. Depth is generally a good thing. One of the problems that has been plaguing the Astros is that they haven't had that depth. They've been forced to give positions to players that didn't earn them or deserve them. Hopefully, with the recent deals for Bourn and Pence, they will have more choices.