What's the best Senran game on 3DS?

Well there's only 2.

Burst has the better storytelling and character development but gameplay is kind of clunky since it's the first one.

Deep Crimson probably has the best gameplay in the series but the overall story is a bit weaker and on the short side and it regresses from some of the character development in Burst. It's a direct sequel to Burst though so you need to play it anyway.