I'd be thrilled to see these four things:
A morale system - much like that in X-Com: Apocalypse, with fleeing foes, units going berserk or panicking, etc. would be awesome. Since you could potentially break a foe, you could put together even larger battles where extermination isn't reasonable and winning by routing a foe a necessity.
Eliminating Combat/Non-Combat Phase Differences
The game operates on a phased combat system. Prior to combat, you can move your guys without worrying about phases, but all they can do is move, sprint, jump, or hold in position. They can't use any of their abilities, special "inspiration" based abilities, or attack.
All too often you have to sidle up to a foe, get into sensor range, then finish a turn just moving and cede the initiative to your enemy . . . even though you know where they'll be and have Sensor Lock as an ability so you could have spotted and attacked them. The game should just do phased movement at all times. I'm tired of basically getting a mech shot at by foes I'm attacking because I activate them with my movement, and then they go before I can follow up on that . . . even if I walked right up into firing range and LoS.
More fixed tonnage missons
Most missions have no fixed maximum tonnage. More should - both by mech size and by total. While I'm playing the Flashpoint campaign with highly experienced mechwarriors, it's just better when I've hit missions with fixed maximum tonnage. I've had to dig into my storage and pull out medium and light mechs and equip them and use them. Sure, I custom configured them and used some choice weaponry - like a Snub PPC++ on one mech and Inferno launchers on another, so I'm still at an advantage. But it's a lot of fun to be forced to use different mech sizes. More missions should have requirements.
Too many say they do - "this mission needs speed" kind of stuff - but honestly you can always just bring 4 assault mechs and make do. Yeah, it's tougher on escort missions, but you core out enemy mechs and ghost their pilots in one-two alpha strikes anyway so who cares if you have to do it at range?
Equip as Stock
If you strip a mech and put it in storage, then take it out . . . you have to re-equip it from scratch. They have buttons to strip equipment, strip everything, and to max out the armor based on free tonnage. But not one to put it to stock loadout. That would be very handy. I don't always remember what stock loadout is, and while I like to customize my mechs it would be nice to get it to show me what a standard Kintaro or Griffin or Catapult has. They don't, and so I just make my own bizarre loadouts. It's fine, but it would be so nice to just grab, click, and then advance time and go when I want to try something as originally intended.
It would be nice to have that wish list fulfilled.