The best indie games like Wario Land 4 are Pizza Tower, Antonblast and Guacamelee 2. Below are 5, each with the reason it is here — and, at the end, what filtering to indie costs you.
Filtering to indie means you want the answer a small team would give. It is usually the most interesting filter on this site, because small studios take the risks large ones cannot.
What you get: One strong idea, explored completely, at a price that makes trying it easy. Indies have no production to hide behind, so the design is exposed.
What made Wario Land 4 worth playing in the first place is covered on the full list. This page is the indie part of that answer, and only the indie part.
Openly built on this exact structure, and the best platformer of its year.
The other modern Wario Land homage, and very good at it.
Transformations used as platforming puzzles throughout.
Transformation-driven 2D exploration.
If the timed escape runs were what got your heart going.
Polish and scale, sometimes. A few of these are rough at the edges, and a big-budget pick will always look better doing the same thing.
Specifically, these are strong answers for Wario Land 4 that are not indie games, so they are not on this page:
The full list is on games like Wario Land 4 — 9 picks, no genre filter.
Pizza Tower. Openly built on this exact structure, and the best platformer of its year.
No. Wario Land 4 released on the Game Boy Advance, but a recommendation is only useful if you can play it, so the picks above span platforms and eras. What they share is the genre and the reason.
Self-published, or published without a large publisher's money. It says nothing about the size of the game, which is why a forty-hour metroidvania and a two-hour art piece sit under the same label.
Constraint. Without a budget to hide behind, one idea has to carry the whole thing — and a small team can commit to something risky that a large one would sand down.
By hand. Each pick was written for the full Wario Land 4 list first, on what the game actually does, and this page is the part of that list that is indie — never a genre tag lookup, which is how "best racing games like Super Mario 64" used to be a page on this site.
Or read the indie guide for where to start in the genre generally.