Sunshine just focused too much on the open area levels. The best parts of 64, IMO, were the more linear levels (like the Bowser stages), and for Sunshine they relegated those to the bonus stages
Galaxy and Galaxy 2, on the other hand, get it right with more focus on the linear type stuff. They do have some openish levels, but the majority is linear.
... And then there's Super Mario 3D Land, which, while fun, almost took the linearity too far. The levels are just short A->B affairs. It works for a portable game, but if you play it in longer sittings it'll stick out.
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Back to the topic at hand; besides some of the obvious ones (Megaman Legends 3), I'll go with... A proper sequel to River City Ransom. Sure, plenty of beat 'em ups since have adopted the gameplay mechanics that really made RCR stand out back in the day (the RPG elements where you improve your character by buying items with money from felled enemies), but a real sequel would be nice.
Japan got a sort of sequel in "Downtown Special: Kunio-kun no Jidaigeki Dayo", which set aside the modern city full of juvenile delinquents and instead set everything in the Edo period of Japan. It introduced some improvements on RCR's engine which would much later see their way into the GBA remake (River City Ransom EX), and there's a fan translation floating around which is also available in several places as a repro cart.
There's also been many other games in the series, but they usually either take a more serious typical and serious beat 'em up approach (ala Renegade), or they're goofy sports games (ala Super Dodge Ball or Nintendo World Cup).
There's also the remake of Rengade for the 3DS that came out in Japan last year, but went with the graphical (and as far as I can tell gameplay) style of River City Ransom, but there's been no sign of it getting a US release, and very little coverage of it online.
