For the classic games if you want to avoid skill shadows and keep timed bombers, the vanilla Lemmix versions are probably much better. You also get the bonus that if you want to use glitch solutions, they are available. Lemmix was designed to mimic the original game very closely, with optional player assist features, so it's the definitive engine for the classic experience without resorting to emulation.
I don't think giving an option to mimic the classic experience would be a good move for NeoLemmix. The original games weren't designed with untimed bombers and skill shadows in mind. These features certainly make them easier, which may be a little disappointing for some players, but at the very least, it doesn't cause content to be more frustrating than intended. The problem with adding the option to remove those passively-active player assist features is the new content.
NeoLemmix offers a number of features like framestepping, skill shadows, untimed bombers, and a lot of the new content is designed with these in mind. At first I tried to design levels that wouldn't require framestepping, but at a certain point, I figured the option is there, pretty much everyone uses it, so I don't test the levels to see if they are playable without it. Bomber placements can be even more frustrating than in the original game with levels that were designed around the assumption of untimed bombers. And with skill shadows and framestepping together, pixel-precise skill placements are no longer important to avoid as long as getting the timing aligned correctly isn't an issue.
The end result is that players using the option to disable skill shadows, use untimed bombers, etc. would need to change these options when playing packs designed with them in mind, since otherwise the levels will be significantly harder than their developers intended, which is, in my opinion, almost always a much worse outcome than when it ends up being easier than intended. The player should not have to tweak their options to play certain content, and level designers shouldn't have to account for the player's options when designing the level. If the player's options have to be considered in the level design, it probably shouldn't be an option in the first place.