The primary difference is the integration with IE Protected Mode (Securable Objects Framework). MSE V2 (both 32 and 64 bit) wrap the named space (lower than standard user space) used by IE's PM in a security layer that examines all packets in and out-bound.
It can create the impression that IE itself is having some trouble with FLASH based Action Scripts, which include relatively harmless JSPopup ad-ware. The handlers are much better and with Tab isolation even badly infected pages, or those seeded with infected ads from external sources may stall, but they won't even crash entirely, much less IE itself. Instead, the page will reload under the warning and MSE will simply block the bad code - so it is like an error, without an error. WEI and the SmartFilters report this and the next time the same bad script is loaded, MSE simply prevents it, so at least for that site/script, the error does not bake the user experience.
Next, the WPF and FSF feature more and bad content is not allowed to write to the temp Interenet files space set up for IE's named space. You will find that a lot of sites use scripts for light boxes and other features that won't run at all - if you encounter this, run them in compatibility mode (again, it's not IE 8/9, but IE 8/9 WITH MSE V2 that blocks these).
Do expect to see a lot more "a problem with this website/page prevented..." <IE from loading> at least initially, but again, as above, just refresh the page and it wil load, less the bad code. It's not that much of an issue, but it does show us just how badly the web has evolved. Treat it the way you would a really nasty public restroom and fully leverage IE's ability to run sites in different security zones. People do not do enough of this - though many speak of the virtues of NoScript in FF, etc.. - never understood that, while they ignore the vastly superior capabilities in IE to trust things at the object level (The Securable Objects Framework/Protected Mode checkbox may be checked for all sites in the Trusted Sites Zone, for example).
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