So, I have an 88key weighted controller I love and I also use an AXIOM 25 (mk1)
I like the AXIOM, I like the semi weighted feel,aftertouch, and the way it has its Midi In set up is easy for me to play my drum pads through. I find I can get it to be pretty expressive with some of my VSTs
BUT, its only 25 keys, its a MK1 so there's no support, and M-Audio USB drivers have issues.

From your personal experience, what would you recommend for a 49-61 key controller?
I would like the same feel, with knobs and faders (for NI VSTs), solid drivers, maybe a little more meat to the mod wheel. After touch, maybe some else for expression control would be cool.

Does the MK2 have all the same features and feel, with better integration and drivers? Or does it fall short?
What do you guys recommend?

I have an M-Audio Axiom 49 mk2 and I love it.  The only issue I had was getting all the knobs and sliders programmed but the Youtube video showed me how.  I haven't experienced any driver issues or any other wonkiness.

Novation makes some pretty good stuff.  The Impluse line is more afforadable, but the SL MkII series may be more to your liking.  The mod wheel is actually replaced with a Mod Joystick in the SL MkII series, which I like better, and you have the option of the mod Pad as well.  It comes with Automap, but I basically use an SL Zero as Midi Compliant.
 
 

I have and love the M-Audio Axiom Pro 61.

The action is fabulous - I did have the faders and knobs set up, but I don't really bother with them.  I bought it for its sturdy construction and really nice action.

Bob Bone

I have many synths laying around but I have used nothing but an older model M-Audio Keystation 88 Pro usb connected to the computer for several years. The action takes some getting used to because the height of the black keys is not quite as tall as on a real piano. Once I got used to that, I was hooked! Great controller for the money!

I have the Cakewalk A-500 PRO, and I don't really care for it. The action is mushy and it has little to no support with non Cake software. ACT has never been easy for me to sort out and in X2 sometimes it works great and sometimes it doesn't.

Harsh but true.

A-Pro has a synth action, not a semi weighted action the OP is looking for. And comparing A-Pro with other synth action midi keyboards or synths, I don't think its action is mushy at all (Tried M-Audio Oxygen?).

I have an A-800 Pro and as a controller I like it. Lots of rotary, sliders, pads, and transport and all very accessible. As a keyboard it's ok.  I actually like to feel of the keys, except they are just slightly shorter than standard piano keys and that takes some getting used to.  Also, the PitchBend/Mod stick is not as easy to control precisely as the older style mod wheels like on my Alesis QS7.1, which I prefer.

Not having much experience with anything else, I would agree with forkol and would at least check out Novation.  I have heard nothing but good things about them for many years and from varied sources.
Happy hunting!