From what I can tell, doing my side-by-side comparison between the MT3E series and the MT3 series (I didn't see a 'premium' version?) on LS's website, the differences are the transmission (E has F8 and R8 (gear) or 3 ranges (HST), MT3 has F16 and R16 (gear) or 3 ranges (HST).). The MT3 has a mid-pto as an option. The MT3 offers a slightly bigger and stronger FEL, and offers CAT II 3pt in the higher HP range tractors.
But thats all I can really tell between the two doing a quick side-by-side. Your best bet would be to consider what you need, go to a dealership and take a look at them. Even if you're not buying at the dealership, talk to them and have them point out the features. Mix that with what you need to have and go from there.
I hope this helps!