Just a quick note, after a couple of quick test missions, I'm thinking the change to the new part stats might not work, for a few reasons.
Firstly, new parts, they've become VERY underwhelming. I think the test missions are the first times where I didn't get even one part that was worth equipping, and that goes both for the big pile of loot, AND the stuff in the store, which is equally useless. The "base" stats between items are often just not different enough to warrant upgrading (or to warrant a new power cost), or also not strong enough. I look at something like the explosion boosters, right, well chances are that a level 5 booster really isnt going to be much different than a level 10 booster (if at all). Maybe a couple of percentage points... but that's it. There's no reason to upgrade until the level is really dramatically higher. On top of that, some part types are kinda worthless with this, the explosion boosters being a good example. I found that most of the time, you needed two or three of those to produce an effect; what made them worth using was the side stats, so they werent JUST gobbling up slots. In the current version, there's no point in using these, or a few other types of parts, as they'll actually lead to a weaker Exo if you take up valuable slots with them. Not to mention this all just being alot less interesting than the way it was before; I can already tell I'd only end up equipping something every now and then, sticking with individual items for silly amounts of time while money just builds up. And finally, with a loot system of this type, the prefixes/suffixes are the entirety of what makes one part different/unique as compared to another. As it is, players will likely keep an eye out for those rare parts that DO have those, and only use those when they can, dropping everything else.
But even more than that, the game as a whole was balanced around the stats as they were before.... and it was working out pretty well, honestly.
I dont think the problem was in the stats themselves; you say that the parts were often confusing and such, and I can agree with that, but it's not the stats that were really doing that, as much as it was the way the stats were being displayed. Example, you've got an Exo who has 20 hacking points, right? You go in, and in some slot, you equip something that has a bonus of 6 to hacking. Well, the window for equipping isnt going to show the 20 hacking points going to 26; instead, it always would show 0 going to 6, because it was displaying only from THAT subsection instead of the main stat. This can be pretty darn confuzzling, and is actually something I kept meaning to bring up (and of course kept forgetting to do, hah). There are other, similar issues related to the way that it displays things. Beyond that though.... there's alot of different stats in the game, and one way or another there might be a little confusion. Stat-heavy games are like that, and it's honestly something that the player just has to get used to with them. I actually think it's not bad at all in this game, if the stats are displayed properly. Particularly since you dont have to go crazy with them when playing on lower difficulties, so the game gives newer players plenty of time to get used to how everything works, and what everything does, and so on. If you go and fix the display to make it less confusing, I dont think you'll have much of a problem.
So, my suggestion is: Roll back this one, and make a few changes to the customize interface and such to make it a little easier to deal with, and a little easier to understand exactly what any part is going to give. That's not to say that there couldnt be a few tweaks to the stats though; for example, a few too many items give boosts to the "ability" stats, like giving you more sentries (as opposed to increasing the strength of sentries, which is very different) or viruses or stuff. That bit is the one that could be lowered a little, particularly on less rare parts. Other than that, I honestly cant think of any problems with the stats and items as they were before.