The T-1000 can shapeshift, is much more durable than Data, and is arguably stronger.
I'm going to call a "not so much" in the durability department when it comes to the T-1000. Now, granted, the T-1000 can take a lot more physical damage than Data (it absorbs an impact and is able to instantly repair it) but there's one area in which Data is clearly superior to the T-1000. Cold.
In T2 we see the T-1000 while being doused with liquid nitrogen freezes (something you have to worry about when your mass is made of liquid.) Liquid Nitrogen is at around 320 and 340 degrees below Fahrenheit. We've seen that Data can survive in the vacuum of space. Which is that cold and COLDER. Now there's a lot of quibbles here when we get into temperatures of space, temperatures in a vacuum and such, but overall we see Data surviving in the cold vacuum of space, we see the T-1000 freeze to a solid in LNi. (The freezing, melting and reforming also caused the T-1000 to have errors in his matrix during the climax of the film.) This means that the T-1000 carries with it all of the fallbacks of being a liquid. (In actuality he'd probably be more likely to BOIL in space than freeze.) Which can give Data a pretty good advantage.
Which sort of brings us to the bigger problem.
The T-1000 is, effectively, magic. He was designed purely to "look cool" and to pose a threat greater than the Arnold Terminator (T-800.) He's an effective machine that can morph it's mass into any shape or form it wants but at the same time is a "machine" while also being "alive" enough to time-travel. We could quibble on what he is, nanotechnology delivered in a "living skin" cocoon, whatever. But considering what we see him capable of and doing he's "magic."
Compare this to Data who is very much "advanced technology" he has circuits, motors, servos, pistons, pumps and has to run off some sort of "fuel." He's a more "real world" device -much like the T-800.
Which is the one problem I have with T-2 the "memeticalloy" the T-1000 is a bit too much to accept. It was handled a bit better in T3 where it was used more of a "skin" over an actual machine which makes more sense and is a tad easier to accept.
So it's hard to really say who would win-out here in any contest. The T-1000 was very much designed to be capable of almost anything (short of mimicking bombs or guns) in order to drive the suspense of the plot. He's a fucking ball of goo that can spread himself out incredibly thin in order to make a seamless transition on a linoleum floor while also keeping the properties of that material (The officer's shoes squeak on the T-1000 like he was actually made of linoleum) and then able to make an incredibly sharp, metal, stabbing weapon. He's actually one big blob made of MacGuffinium.
Love T2, but you have to admit, the T-1000 makes no sense, thankfully the movie is good enough to make up for that.
Data, however, as inconsistent as his abilities could be was still a machine and at least had those limitations that were held mostly consistent.