My main issue with TC4.1's system is that it's two-fold repetition. You have to scan items in the world and do the minigame to get to the end, neither of which are spectacularly engaging beyond the first few tries. Plus the "easy" mode isn't really balanced to the aspects available (which made it really difficult in something like Agrarian Skies). I'd quite like to see the option to "burn" research points to avoid the mini-game, or use them wisely when needed.
To be honest, I'm somewhat surprised that none of the packs have offered a "quick route" through HQM (offering the discoveries as rewards for certain aspects of the quests). It's been something I've been tempted to try making, but not gotten around to it.