What software are you using for the animation?
Nahton introduced us all to Fragmotion (which has a free version) and he had a fair bit of success with it. I always struggled with Milkshape's idiosyncracies on the animation front.
My first choice is Milkshape3d; I do really hate the issues you know too well (unusual axis arrangement, skin folding in the most unsuspected ways, bones rotating around the wrong axis, and so on), but it's good enough and comes in handy for basic animation, and I like its keyframing tools.
I've been using also a very old 3ds Max 2008 I bought years ago when I was mad about flight simulation and virtual cabin modelling (those were far better days from a budgetary point of view!), though has got some very annoying graphics glitches on my current computer, so it's a PITA to get some work done, needing to restart now and then.
So now I'm giving a try to Fragmotion, which seems to have potential, though at first sight I think it's somehow less intuitive than Milkshape. If it's worth the $50 the developer asks for, I think it may be an affordable option to take into account.
ars longa vita brevis - Hippocrates (attributed)
If you want to tell jokes then use Muvizu; if you want to make 'Movies', use iClone; but if you want to tell stories, use Moviestorm - PrimaveraNZ
Shared addons & stuff for Moviestorm: https://drive.google...aTNsSFBuN0sxZHM