I'm in the same boat. I've been nervous about this plugin, as it is entrenched in my site.I held off on upgrading, though, to see if anyone else had problems....
So, based on the problems I see, I am messing with a workaround. I haven't gone all the way through this yet, but here's what I am thinking.
I installed the shortcode exec php plugin. It will do php and html like sniplets. It seems to work when entered in custom fields and pulled up in the post php. (I use a custom posts plugin from before custom posts were part of the core, and i use custom fields as a CMS.)
I dumped the sniplets table from phpmyadmin, and put it into the word 2000 format. It keeps the data intact best for copying and pasting.
I exported a shortcode from the exec php admin page, and then pasted the content from the table into the xml file and imported it. It worked, so I am thinking of trying to concatenate the heck out of the code in excel to eliminate the cutting and pasting.
now, the part I haven't tested is that I am going to try using 'sniplet' as part of my shortcode name (added when I do the concatenation mentioned above). The shortcode exec php plugin works with two words with a space for the name, so i am thinking if I disable the sniplet plugin, the existing commands would not need to be changed on all the posts. Does that logic seem to hold?
Any thoughts on this late-night ramble?