At this point I consider myself to be a Keynote veteran, but I'm still fairly new to Keynote on iOS. I've given a few presentations using my iPad Mini hooked up to a projector (or a display), and using my iPhone as the controller. The animations are kept intact and the slides are largely unchanged. The only things I can think of are that occasionally the text looks slightly different (the default font that Keynote uses is apparently not available on the iOS version, so iOS uses a substitute; you could easily fix this by manually changing the font to something that iOS has), and one transition effect - mosaic with the scale effect - switches to standard mosaic. Magic Move, the most important transition effect, works perfectly.
As a bit of a tip, export to Quicktime. Most Windows computers have Quicktime installed. This allows you to retain your animations, and Apple apparently have something built into Quicktime so that it pauses at each slide transition point until you press a key. Once it's fullscreen, you might as well be presenting straight from Keynote itself. The biggest difference (aside from no easy way to go to a specific slide) is that going backwards through slides results in the animations running backwards. With Keynote, going back a slide simply goes back, without any animations.
Also, Apple produces Lightning-VGA adapters so that you can hook your iPad directly to the projector, and project off of it. If your school uses fancy projectors, there are also Lightning-HDMI adapters. The adapters are fairly expensive ($50), but if you use it regularly then it's worthwhile. As an added bonus, few people seem to use them, which gives you some shock value. The iPad to projector + iPhone slide remote setup amazes people every time I work it. It gives you a running start to grabbing people's attention and having a positive perception to your presentation.
To answer the question you posed, however, I must admit that I have never made a Keynote presentation from scratch on the iPad. I've made minor tweaks to presentations, but I think it would be painful to start from scratch... although I suppose it depends on what you're presenting, and how complex you get with your visuals and animations.
I'm in the medical field, and I use a similar setup. If there's no projector around and I'm with a small group, I can usually unplug a monitor from a nearby computer and then "project" off of that, allowing the group to sit around the computer while I stand behind them (so as not to block the screen) and present the topic. It's surprisingly useful!