Sometimes I think that it would be best if they simply got the mech variants from the Record sheets/TRO's and closed the mechlab.
Though I suppose that tons of players would be boned if they wanted to remove a medium laser to mount a C3 slave.
Remember the good old MW2: Mercs days? You actually had to pay C-Bills to customize your mech. A complete rebuild cost you almost as much as buying a new mech.
I'd personally implement the following for mechlabs/repairs/salvage:
1. You can customize your mech as you see fit. But you would be limited to what you have in your inventory. Wanna install a new pair of ER Medium lasers to replace the old ones? Buy/salvage them and then install them.
2. Shortages could be problematic, you can't always build what you want. IIRC, MW2: mercs at one point had a shortage of PPC's and later LRM ammo. Things like these would draw the game closer to the BT universe.
3. Getting your mech completely destroyed should force a player to pick a new one from their faction RAT. Any changes made to the previous one would have to made again on the new one (which costs money again). It would be nice if you could store a template for this.
4. You can only repair components with parts your techs can support, you can't put a Clan ER large laser in your IS mech in 3050. This would ofcourse become a different story around 3052.
5. Players shouldn't be able to alter stuff like engines and internal structures. Swapping out weapons, heatsinks, jumpjets and equipment like ECM or BAP should be the only options.
6. Any mech can have jumpjets, ECM, BAP, etc. MW4 locked this out for a ton of mechs whereas there is absolutely no reason to do this in the canon. You couldn't even build a Timber Wolf Pryde for crying out loud.
7. There should be match types that only support canon-only mechs for the hardcore players.
8. No more coolant flush, be smart about how you use your weapons, it'll come back later to bite you in the ***.
9. Depict the OmniMechs like they should be, they can get different loadouts inbetween missions whereas regular BattleMechs are limited to places with fully functional mechlabs.
10. The mechmarket or whatever should spew out newer variants or mechs as they are produced. The Master Unit list was recently updated with production dates for all of them:
http://www.masterunitlist.info/
11. The TT mechlab would also bring back important things like locations where equipment is stored, you could knock out a ECM or heatsink by targeting the bodypart it is located.
12. Salvaged mechs would need to be repaired with parts you buy, mechs aren't magically restored in two weeks time. It would be virtually impossible to repair Clan mechs due to a lack of parts. It would be best to sell that salvage to the Successor States and make a ton of cash.
13. Not all mechs can be repaired (due to turning into a mini mushroomcloud), but they can still be scavenged for parts (your new spare parts).
14. You shouldn't be able to simply buy and sell parts when you are behind enemy lines. Think MW3, you are on your own, anything you couldn't use got dumped somewhere.
15. Your dropship/base is your lifeline, getting that one destroyed will leave you without any repairs/reloaded ammo in the next mission (assuming that some missions are linked mini-campaigns). Any customization would also go out of the window here (until you get back to a friendly base atleast).
Just my two cents.