I have a 01 Impala Auto, and we put a brand new trasmisssion in it a little less then 2 years ago, and its starting to shake and mess up when shifting up... I highly doubt it's the transmission, so what else could it be?

It's the transmission. There is nothing that I know of that would exhibit the symptoms of "starting to shake and mess up when shifting up". Apparently that tranny needs attention fast.

I have a 01 Impala Auto, and we put a brand new trasmisssion in it a lil less then 2 years ago, and its starting to shake and mess up when shifting up.... i highly doubt its the transmission, so what else could it be??
Is it running poorly? A serious misfire could cause some of these symptoms...
How many miles? And when were the plugs inspected? Filters etc?

How exactly is it "messing up" when shifting? Is it sputtering or making noise? Is your check engine light on? Like Captain said, it could be a misfire problem.

How many miles have you put on since you installed the replacement transmission? Have you had the filter & fluid serviced since the replacement?