Atomic Browser is capable if identifying itself as IE. That doesn't give it any of IE's features. Think of it as lying to the web pages it visits so that they don't know it is a mobile browser and sever the big boy pages. Like most youngsters, that doesn't mean it can always handle what it gets.
There are several third party browses with features and interfaces different from Safari. You can give them a try. Besides Atomic, the iCab and 360 Web Browser are very popular.
For limited Flash you can use:
iSwifter
Skyfire
Puffin
These basically use a remote server to redisplay the pages for you.
No mobile browser is going to give you all the feature and abilities of the big desktop versions. For one, the market is only a year old. Apps have to mature. For second, it's a lot like trying to cramming a V8 diesel into a Honda Goldwing (motorcycle). I'm sure it can be done, but no one has been ingenious enough to manage it yet.
There is one workaround. You can use one of the several remote computer apps to control your desktop from the iPad. A couple even offer the ability to do so over 3G. Several of our members swear by them. YMMV
