1) There appears to be a bug that drains $$$ that kicks in after a certain amount of progress has been achieved. For example, when I check 'Manage Economy' at the current point in my game, I'm at -$77/day. I click End Day and $266 disappears from my finances (with no events happening to explain the extra $ loss).
2) I feel the greatest strength of the game is how open-world it is. Especially to begin with, there are so many options available. I would suggest that to improve this, and to keep options open late in the game, you could add a gambling minigame or two, where players can wager either money or crafting parts, with the option of wagering higher stakes as the character becomes more influential. There were some excellent, replayable minigames in computer games of the past, such as Arcomage in Might and Magic VII/VIII - which strikes a fine balance between strategy, luck and unpredictability. A current MMO, Renaissance Kingdoms, implements a Texas Hold 'Em poker option within its taverns. Perhaps something similar could be implemented to enhance MoR?
3) Gameplay gradually becomes more repetitive, and you end up having to grind in the arena to build cash or grind in the crafting skill to produce items. To produce more variety in encounters later in the game, I suggest adding more random NPC spawns at different places on the map, with greater variety in rewards (e.g. crafting parts, ammo, armor, tendstims, books to raise academic skills/intelligence, serums to inject slaves with that increase/reduce certain stats).
Overall, this is one of the best, if not the best, RPG I've ever played, and I look forward to its completion.