Some are quite specific and I did just think of a good reason to 44A+Bg now.
Do share it if possible. I'll make a brief summary of why I picked those moves:
3K: just feels pointless. Raph has more reliable mids at all ranges, like 3B for damage/pressure and 3A for tracking/zoning. Does 3K even track at all?
33A: lacks range and it's very unsafe, low reward, TC frames unreliable. At that range you have much safer tracking moves like 2K. If opponent is gonna step into a TC move or a duck, just wait and punish.
prep A+B: I have explained multiple times why I consider this move to be useless (outside of the combo). But I feel like it's one of these moves that are underestimated. For example, the start up animation of this move is quite similar to a SE entry. When I'm focusing on beating SE on reaction, I fall for prep A+B almost all the time. Might be worth investigating (or maybe I just suck).
44A+Bg: I personally never use it because the amount of time it takes to put Raph in prep is more than enough for opponent to come in and beat it. But it might have potential if I find a way to mix it up with 44A+B.
66K: sure, it's good for ROs after guard breaks. Other than that, I forget this move even exists.
11BB: Raph has stronger and safer lows, and 11K is better for oki mixups. Also, there's always a better combo ender possibility than using this move.
wrA: When I'm in FC and I have the advantage, I try to mix up with a mid (wrB/FC 3B) and a throw. I end up forgetting about wrA and wrK completely most of the time, because a throw is better for any situation these moves might fit.
6AB/prep AB: I don't think they're "useless", I just never use them excluding rare occasions and combos, mainly because of range. Definitely a move I need to use more.
66A+Bg: I don't need to explain this one.