Write your own? I'm sorry but if Bundler doesn't solve your problem (or introduces other problems) either try and fix those issues OR write your own dependency management lib.
The unfortunate reality about writing your own new Bundler is that you'll inevitably end up rewriting Bundler. Isolate is basically just a mini-Bundler with a different (arguably simpler) storage location, but the storage location is really not where the complaints about Bundler are coming from.
Rewriting things just to shed complexity or "bloat" will often just put you in a position where your library just can't do things it will need to do, and then you end up rewriting those things and adding back the complexity. It's the circle of life. Lack of SCM support in Isolate is a good example-- I'm pretty confident that Bundler's support of git is heavily used and taken for granted, but if you were to rewrite or use a simpler dependency manager, you're throwing this out.
This point feeds back into the larger issue of Rails vs. Node, I think. Rails ended up with all the complexity it has now because it was [mostly] necessary-- not all of it was, but much of it was. The idea that you're somehow liberating yourself by shedding complexity is often just the short-sighted pleasure of running faster test suites. And it's usually followed by a little bit of claustrophobia when you realize you can't do X, Y, or Z anymore. Wait until the claustrophobia kicks in, because it will. And the solution to this claustrophobia? More cowb-- complexity.
I agree. I just hate to see this ― "zomg bundler sucks at <some feature usually speed>! I hate using it! It has to be fixed for me!"
Any open source project needs help. The maintainers of Bundler have 200+ issues on the issue tracker. If people could help them replicate and confirm issues, write failing tests and if possible write patches ― it would do a world of good. But instead it's EASIER to complain and whine. So...
