I think most rules nowadays are fairly base agnostic, including the two you’ve mentioned.  I’ve played both Bob Cordery’s various rules, and the various Rampant series from Dan Mersey with both element based forces and individually based.  (For the Sudan specifically, I’ve used both 15mm element figures, and 28mm round bases…and also for Black Powder, Patrols in the Sudan, Sharpe Practice and a bunch of others I can’t remember.  They all worked no matter the basing!)

It’s easier to play with individually mounted figures, as you just remove a figure for a loss.  With element you must use a slightly unsightly die or casualty cap to track losses.  On the other hand, it’s a little faster to play with elements because there are less things to physically move.

I find – and this is entirely subjective – individual round bases look better for skirmishes, square look better for nice, neat formations drawn up in rank and file.

As I am forever trying new rules, I’m a bit leery committing to that 3-2-1 system of Michael Lecks.  My best compromise has been to mount figures individually on round bases…but then to use sabot trays to move them about.