From my perspective, I'm dumping a useless bench player for a serviceable (albeit old) bench player. Granted, Fukudome is making slightly more than league minimum ($19k more, to be exact), but he's a vet... that's a pretty good deal for a good utility outfielder. I can't see Pena being good enough to stick in the majors ever, which makes his major league contract a problem (he's eating up a 40 man roster spot).
Really, the problem here is the same as with all games: the AI doesn't have an overarching plan at all. Mogul has the same problem, in that to the AI all trades, signings, and draft picks are evaluated individually. There needs to be an overall AI object (in the programming sense) that looks at the whole team structure and devises a plan. This isn't rocket science, it just needs to be done!
But yea, things are better in the last couple of years. I don't dispute that at all. I'm just slightly frustrated because there have been hundreds of us saying the same sort of things regarding the AI for years and years now. *sigh*
Oh, and by the way, here's Fukudome's contract:

Which is great, to me. I mean, I'm in complete control here. If he falls off the cliff towards the end of the season I just buy him out. I can certainly deal with a $3.5 mil contract for a part time player, though... and so could Chicago, really.