Yes.
UI is better, better set up, dedicated movie button, C1-C3 can auto-update, instant jump to 100% view and back, histogram is outlined so it shows up outdoors, in cam RAW processing if you need to suddenly process and send a raw to someone in the field (rare, but nice when needed), more powerful MFA, etc. (only bad thing is zooming in to view during movies is worse since the button is in a bad place and the move to SET that works wonders in stills modes seems to not work in movie mode)
AF is better, at times for some things, much so
movies are better with better SNR and no moire (but a touch soft and they left out way too many options,
although ML is bringing, but not all of them back)
fps is much better
less mirror blackout and faster trigger response
high iso shadows are less ugly, sometimes makes a huge difference, but certainly not always
SNR is 1/2 to 2/3rds of a stop better (taking into account that each ISO on it applies almost 1/3 stop more gain than the same number on the 5D2), modest but every bit helps a little
LCD is better and has more accurate colors (not THAT accurate but not the disaster of the 5D2 LCD), shows up better in the sun
build feels a bit better
while not as crippled, AutoISO is still totally crippled (ridiculous nonsense from Canon marketing dept.)
low iso DR is not improved at all

technically it is actually a trace worse even, the single biggest disappointment in the camera perhaps
no replaceable focusing screens

MP are merely the same so no extra detail like on a D800 or reach like on an APS-C or D800
it certainly works better and is more usable, no doubt at all, much more of an overall joy to use, so it is certainly an upgrade, well worth it (unless you do only tripod-based landscapes, in which case it's not worth it in the slightest really), just a bit of a shame the low ISO is not even as good as the old 1Ds3 low ISO nevermind anything close to D600/D800 or even D4 for pixel quality and they did a few silly things like with autoiso and leaving video features absurdly bare bones and crippled (but thankfully ML already fixes some of that and will fix more so that will help a ton, but it can't fix quite all of it)