Less customising can be done.
Has no built in midi outputs, so can only use the USB to your laptop and not attach a midi master keyboard for example.
Mikro has no direct push button access to group functions and you need to access the groups via a secondary key shortcut.
Mikro cannot adjust multiple parameters at once, but you can add a secondary midi controller and do it from there.
So all in all I would get the standard maschine if you care about those functions. If you just want to play around and use it as an F1 on steroids, then go for the micro.
As for Mk I or II: If you like multi colored lights then go for Mk II, I can do without them, but the Mk II is more fancy.
Well the colored lights give you a lot of “color coded” info for which you else would have to look on the screen or displays. Like modes and such. But it is something I would consider “nice to have” but not a dealbreaker if it is not there.
The software features and expansion packs work on both. The only difference in the Mk II is that the knob arrangement is somewhat different, so accessing some functions is a little different in both generations, but everything is still there…