We are currently reorganising the code. The upload functionality heavily depends on how wordpress implements it. For our sake, purpose and point of view, the WordPress media functionality sucked. So, we made some modifications.
That was 3.4 story. Luckily, the media in WordPress 3.5 has changed wonderfully. Once we are done with the code restructure (2.4), we'll be revising a lot of code, fixing bugs and adding a few enhancements. We will be rewriting uploads in 2.6. This will happen faster than our earlier updates because of the restructure.
Unless, it is highly critical, could you wait for a fortnight or so, for us to switch to the brand new upload? If the WordPress new media uploader works for you, ours will work too. It will be that similar.