Disclaimer: I run the second largest Mechwarrior 4 league Ristar (which, BTW, runs on 100% Free software :) ) I also am a Mechwarrior veteran of about 6 years, starting with Mechwarrior 2 (netmech DOS) on Kali.
We'll just jump right in - They did several things right - for starters, you can no longer destroy a mech's legs. I agree with this completely, as it was very common for low-latency connections to simply stack up about 20 ER Laser(M)'s in MW3 and then blow off an opponents legs.
The leg does get destroyed however it just dangles there and can still be used to "limp". The big improvement is the Mech itself does not get completely destroyed when one leg is destroyed as it did in Mech3.
What I disagree with is the more automated nature of some of the weapons, and the inability to use the mouse "inside" the cockpit to zoom in on things. I don't know what's going on there, but that was a major, major feature and I want it back.
This functionality was not really "realistic". In a "real" Mech the arms only have 45 degree lateral motion, not to mention that weapons mounted on the torso have no actuators at all, the only way to aim it would be to twist or pitch the torso, like on a tank. Mechwarrior, like it or not, is supposed to be a simulation game of fantasy futuristic giant robotic tanks and therefore should be as physically correct as possible. The floating reticle wasn't.
Many weapons are fire-and-forget in MW4, perhaps a concession for not being able to use the mouse for target aquisition anymore. For those of you used to lasers, you may wish to reconsider using them on heavier mechs.
I can't remember one weapon from Mech3 or 2 which wasn't fire and forget. The only weapon in Mech4 which isn't is the bomblast laser which charges over time and fires once it's charged, which makes it pretty useless.
The other big complaint I have is that they no longer allow you to create "boats" - mechs with only one type of weapon on them.
Not true, you can make boats. Good boating chassis are Catapults for missiles, Novacats for lasers and Daishis for LBX and generally any Clan OmniMech.
In MW4, this tactic cannot be used because the weapon slots are now reserved for specific weapon types - they are no longer generalized.
And on Clan OmniMechs you have Omni "hard points", which allow you to place any type of weapon in them. I like the new hard point system. It gives roles to mechs instead of making them "x tons bag-o-guns" as one develloper put it. In league play this really stands out.
My biggest complaint, however, is the way they put the radar display together - switching to terrain mode hides a variety of necessary things, and there is apparently no way to modify the ranges
You can zoom the radar range in.
My last major complaint is the weapons display - it is friggin' impossible to tell what weapons group you are using, something which is absolutely critical when you are in battle - cycling the weapons change past the slot you wanted could spell death.
The game was designed to be played with a joystick, (so Microsoft could sell more) and this "oversight" isn't such a big problem. With joysticks you can map 3 or more buttons to weapons groups, and just press one to fire certain groups, no cycling required. For mouse users I suppose it would be more of a pain.
My biggest gripes are the bugs: third person perspective gives aiming/locking/firing advantages, gamma can be used to negate night, shooting through mountains, destroying one leg then shooting the destroyed leg again kills a mech, every once in awhile it'll drop you into the game with the stock variant of the chassis you picked, not your custom, etc. If they'd fix the bugs the game would be really nice, trying to "legistlate" around the bugs for league play is really horrible.