So one more annoyance for the pile:
When you assemble a mech via scrap after a battle and the interface comes up saying which one do you want to replace/store/scrap, it does not indicate to you which mechs are the ones you have customized. If I have two Grasshoppers and I want to store one, I have no way to tell (unless I remember what the firepower amount is or something) which mech has all my custom bits on it. So if I accidentally pick the wrong one, I have to refit the other mech.
It's also very dumb that salvage assembled mechs get free weapons. It totally disincentives ever bringing a mech out of storage really both because you don't get the weapons if you store it and when you bring it out it takes additional time to refit since they come out of storage blank. It's almost like no one tested this.
The game undermines quite a lot of its own mechanics this way actually. A few more examples:
Player character can't die, cool but if you get 5 injuries it's gonna take you 8 years to heal so you might as well load anyway.
The salvage vs money system in negotiation - So in theory you can take less money or less salvage or both for reputation benefits. But the reputation positives you won't see until later and they aren't good enough to outweigh the initial benefits of more salvage/money early in the game for the snowball effect. This feels more like a half baked mechanic than one that's completely undermined, but it could be somewhat fixed by exaggerating the effects on both ends. Bigger rep bonuses for taking a discount on missions (but the faction on the other side should get really mad about that) and better discounts in the store.
First point, just rename your 'Mechs. You can do it on the 'Mech bay entrance screen (near where you change the pattern). Then you'll be able to tell.
HBS hasn't really commented on the second one (they're not like Paradox in the sense they respond to design debates on the forums), but from their perspective on the issue of difficulty, you can see why they did it. First, by having to build up a 'Mech from scratch, you're basically making it impossible to field new 'Mechs at the start. Second, it's very good for new players to be able to get a new 'Mech ready to go right after a contract. People hate that games cater to "casuals", but BattleTech has a very steep learning curve. You should scare away lots of players without these features. Currently, you can strip a 'Mech yourself and simulate that it came with no weapons (you almost certainly have all the same weapons anyway, and if you don't, you can always sell them because they're more or less worthless). I'm willing to bet on an Ironman mode that HBS said they're working on for the summer, this is going to be a feature.
The reason the player character can't die is because it would be instant game over. The story works around Kamea hiring you because she knows you. They talked about medical retirement that might make it into an ironman mode (i.e. you don't die but you are medically unfit to pilot a 'Mech).
The way I've interpreted the reputation slider is for post-game contracts. You have a few factions that offer very few contracts, and when you're seeing mostly 4 1/2 and 5 star missions, you're going to be gated by reputation to take the big ones (all the major houses have missions that require allied status and 1000 MRB rating). Rather than having to jump around the map searching for the lower tiered missions to build rep, you can take only rep to build it quickly.
Absolutely the game could use more fleshing out, but they needed to get the game out now to make some revenue so they could gauge the player response to the game (which has been positive) and whether it's financially viable to make more content. There's a lot they can do with missions specifically and that's something they've mentioned in post-release roadmaps. Talked about multi-tiered missions, missions where you fight "unique" groups (other mercenaries, elite guards, famous pirates) who will remember you, diverse mission types, etc.
