Thank you for all the detailed comments. This is exactly the sort of stuff needed to demolish problems in the original game and make a better start on something new. I haven't been working on Redux lately, but when I do return to it this will be quite helpful.
One thing to note on some of the recruit irregularities you mentioned-- some unresolvable bugs in the game engine affect the recruit pool. Recruit perks and skill points are randomly distributed when the game autolevels the soldiers to more closely approach your main character's current level. The workaround, though piquant, is simple. When you speak to the Recruit Master, if you hear the 'level-up' sound effect this means the game has autoleveled some recruits (most likely in a way far less than optimal). If you look at a recruit's stat screen and see that he/she has levelled up beyond the point where you last used them in a mission (or if you have never used them), simply exit the recruiting screen without hiring anyone and then immediately speak to the Recruit Master again-- all recruits will be returned to their (lower and thus more customizable) baseline experience level or otherwise to the experience level they were at when you last took them on a mission. Sadly, nothing can be done to fix this original game bug.
I usually try to find some recruits I like early in the game, and keep them with me for multiple missions so that I can shape their perk/skill development rather than allow the AI to randomly decide their advancement. I believe this is by far the most common style of play. Yet you sound as though you enjoy the variation of using many different personnel. There is certainly nothing unreasonable about such an approach, and you're right that additional accomodations need to be made to such a style of play than is currently offered. In other words, the remodelled recruits still need a fair bit of work to differentiate them from each other in a way that makes each one of them a potential asset under various styles of play.
On the turret lootable ammo issue, this is another original game problem. I didn't look at it too closely, because the game generally has an incorrigible surfeit of all manner of loot but the quartermaster system should work to rapidly bring the marginal trade value of any items traded in even modest quantities to near worthlessness. With any particular vendor, once they have even one of a particular item in their inventory the price they're willing to offer on each additional instance of the item plummets. As you noted, however, this is rather less noticeable on ammuntion as opposed to guns and armor (because thousands of units of ammunition are typically involved, even a pittance per unit can add up to something significant). On the turret rockets you mentioned in particular, however, there is the practical matter to consider of weight and inventory limits. On one hand I'm inclined to say if a player actually has the patience to make numerous trips back and forth across a mission map to gather up all the loot, and then has further patience to micromanage a vehicle inventory, and then has yet more patience to make numerous trips back and forth from the vehicle bay at a bunker to the QM station to barter away the loot given modest carrying capacity per soldier per trip, he really does deserve some sort of nontrivial payoff for all that effort. If a player is really having such difficulties that his team needs the cash badly enough to justify such herculean looting of maps, perhaps we ought not remove such a safety valve mechanism.
I agree with your comments on lockpicking-- believe it or not, I already did a fair bit of work on making doors and containers susceptible to lockpicking in order to increase the utility of points spent on lockpicking. The approach of the original game was apparently to consider most doors as simple scenery that no one would ever try to open-- hence the considerable number of doors found on original maps that would say 'does nothing' when one used lockpicking on them. Another problem was that a number of doors were not lockpickable because they were meant to use particular keys the player-characters can find on the maps, but the devs either forgot to place the keys at all or placed buggy keys whose tagnames did not match the doors they were intended to open. I changed many of these to be fully functional doors (even if very difficult indeed to successfully pick in the case of doors needing a special key because opening them offers a remarkable tactical advantage), but this is yet another area where much more work remains to be done.
You're absolutely right about the countdown/run for the blast shelter at Cheyenne Mountain. Beyond fixing glaring bugs, increasing the general player-friendliness of the game was among my top concerns while designing the mod (hence among other things my several clarifications of the player's otherwise obtuse objectives on the subsequent maps inside the mountain; if this is your first time playing you were hopefully spared a severe case of head-scratching about how to proceed that afflicted me when I first played years ago). Your suggestion on this point will definitely be implemented in a future version.
Thanks again for the comments, and please feel free to report all matters you feel need are in need of attention as the game can only benefit from a consideration of all such issues. Our putting any thought at all into many matters will apparently be more thought than the original designers could be bothered to put into numerous aspects of the original game's design. My general thinking on this subject was that when I saw something I didn't like, I'd make a change based on some minimally definable principle in the hope that even if the reason for any particular change wasn't the best idea a consensus for a more reasonable basis of improvement will subsequently emerge from community discussion.