There are three big things I can't stand about the X series:
1. Out of sector combat gives totally different results from in sector combat, to the point of small groups of M3s managing to somehow blow up capital ships.
2. In-sector AI is terrible. Absolutely, positively, horrifyingly terrible. This becomes readily apparent if you ever attempt to fight a battle as a carrier ship, since your fighters will crash into your hull when told to follow you - killing themselves and stripping your shields. They also do this if you happen to have a fight going too close to your ship. Or if you look at them funny. This can be reduced by using slow fighters (or not upgrading the speed of fighters meant for the AI), but it's still very annoying.
I guess 1 and 2 may be related, in that #1 assumes the M3s are far smarter than they are, and #2 has them waddle around and get shot (or slam into the ship they're trying to fight, which is less effective than one might think).
Oh, and for the third thing:
3. The economy is extremely shallow and broken. Without the player's intervention, few if any of the AI controlled factories ever get enough supply to produce much of anything. Theres always a huge demand for just about everything just about anywhere, because the AI traders don't ever really accomplish anything. They spawn endlessly and fly around, but generally their cargo rarely reaches the target and they either die and respawn somewhere or just sit in some station for ages. On the other end of the spectrum, the player can produce limitless amounts of pretty much whatever they want, and as long as he prices it low enough the AI will magically spawn traders to buy it in droves, even if the only way into the sector is through xenon territory where all the outgoing ships die (and then respawn and buy more). You can do this with loop complexes that produce everything they need to output large amounts of an end product.
Like I once made a gigantic electronics manufacturing complex, making more electronics than every factory in the universe could have possibly used, without any outside input required. It was made to do the ridiculous resource collection quest in the game, but after that was done it just sat there churning out more money than I knew what to do with - because no matter how much crap it produced, there was an endless stream of traders coming to buy it because it was priced at the minimum. Although, to be honest, I did find things to do with the money - mainly due to the fact my capital ships kept dieing to pirate novas while out of sector, and the only way to prevent it was to make super fleets that could have conquered the universe (if it was possible to actually conquer anything in the game, that is).
If they could correct these things, it could be a really good game. If this game ends up with the same shortcomings, I'm going to be very disappointed.