I absolutely love Skritter. If I had to change one thing about it, it would be the site speed. Certain pages load really slowly, which takes away from the time I should be studying, which is of course the main point of the site. In particular, I've noticed the following (in order of priority):
"Study/all" page: The blue/green graph at the top, showing "X to review / Y added," is not very helpful. For one thing, I'm not sure what "added" means. Added since when? For another, neither of these data points really means much to me. There will always be more to study, even if I somehow get the "X to review" down to 0. Also, the scale is inconsistent. For instance, right now, my graph says "103 to review / 90 added" but the blue "review" bar is about 1/6 the size of the greed "added" bar. And, as The Professor just told me while typing this (nice), the review bar can be a little inaccurate. I'd happily do without this graph if it would speed things up even just a tiny bit.
"Vocab/listsec?" page: Even the official and textbook lists take a long time to load. I notice there is a ton of Javascript on these pages, and I wonder if some caching of the standard lists would help. Maybe the progress could be loaded only after clicking a button, so at least the rest of the page comes up more quickly.
Main "/study" page: There are a lot of graphs and things on this page that seem to slow down the loading. I would totally be willing to give up the whole "X words to study in the next 5 days" section if it would speed the page up by a millisecond. The blue/gray area graphs are pretty meaningless to me, and I'd opt for a cleaner page anyway.
I know each of these things probably doesn't impact the speed of its particular page a whole lot. But I wonder if removing some of this dynamic content (or requiring a button click) would reduce your overall server load and make the whole site a little faster.
To me, the most important features of the site are the vocab lists, studying algorithm, and the practice page. Any bells and whistles (and graphs and server calls) that slow these features down even a little bit is probably not worth it. It might be different if you had Google-type data centers and CDNs. But with the resources you have, I'd try to focus more on site speed. And that iPad app! :)