You should definitely consider as anweRu mentions knocking down that university and replacing it with a church. (Poland and Prussia have different religions right? If not, then a spy building would probably be better.) Not only will the church add a happiness bonus, and a quicker religious conversion, but the university is probably causing unrest. Of course, the downside is that it's one less place to get research. I also find that the AI is able to build top buildings quicker than I can, so depending on your build and research priorities, that university might be your best research facility!

One thing that's different for me in ETW is that with the new rebellion system, I've learned that sometimes, you just have to tolerate a few years of rebellion when capturing major cities. In previous TW campaigns, I would consider it to be a giant failure if I allowed a rebellion to happen. In ETW, a rebellion doesn't mean you've lost the entire city, it just means having to pay for some repairs and fight off some rebels.

In my experience, rebel stacks are usually pretty small (~ 8 units or so), are pretty low quality (mostly militia, maybe a few units of light cav or 1-2 fixed arty), and have no general.

So that means two things. If you let them rebel you can:

1) Leave your whole stack in the city, and you'll be able to crush the stack with few losses.
2) Leave a rearguard in the city and move on. How many troops you need in your rearguard will depend, but assuming Warsaw has walls, I think 4-6 line infantry; maybe an arty unit and some light cav to run down routers will do it. One downside of defending vs. rebellions as it seems that the town watch won't come out to help your troops.

Two other tips:

1) A few priests moving well ahead of your army can help somewhat.
2) If the city is going to rebel regardless, no point in giving them the tax exemption!