- there can only be one instance of the programme running at once (I like to make different versions of a design and compare them)
- I have to have the CD in the computer to run it.
Once upon a time this would have been standard, how times change

- I'd like a more up-to-date thread palette, another vote here for variagated threads.
I agree with the comments about the erratic undo function. To this day, I have not worked out how to undo backstitches at all. The nearest I have got to this is to put cross stitches on top of the erronious backstitches, which sort of hides them, but it's not ideal. Also, I sometimes find drawing tool selection a little clumsy. Both of these I can live with, though. It's a shame there are no evenweave options, but it does at least have linen.
I don't trust either the onscreen or printed colour representations to be accurate, but that's not just the software and I wouldn't rely on the colour representation whatever the programme. I have a DMC colour card to look up colours more accurately.
Other than that I've learned the hard way that it's best to use image manipulation packages to clean a photo up before importing it as a pattern. The only photo I've imported which I got right almost straight away was a very old and very simple black and white portrait.