- Nasty yellow subs - I don't think that I've come across a DVD where the subs themselves are as visually appealing as those on other versions. I don't know enough aout DVD authoring to comment on what limitations there maybe.
IIRC the DVD spec only allows for a handful of safe fonts (in a handful of sizes), for them to be static, and only for 4 colours total to be used - normally done so you have two contrasting colours for easy reading on most screens (an outline, filled with a contrasting colour).
The positioning is also done to allow for the fact that a lot of older screens have "overscan" which means you can only put subs reliably in a certain area of the screen.
Things like the ADV vid notes, jiggle counter etc are all really pushing the spec (iirc the jiggle counter was in part a way for ADV to check that vid notes would work, as it used the same coding).
Remember DVD specs were set something like 10 years ago and for a disk to be classed as a DVD it has to abide by them, and even then there are some players that don't like certain things (PS2 i'm looking at you

), so has some fairly serious limitations in what it can manage in terms of anything other than normal playback of the A/V Streams.
Fansubs can manage different things because they either hard encode the subs etc onto the image (something DVD's tend not to), or because they are using the processing power of the PC to do various things (hence the fun and games with codecs at times).
I think it's Animeago who have a very interesting set of notes/articles on their site about how/why they do some things the way they do.
They started using the two contrasting colours per sub, with up to two sets on their original VHS releases due to a combination of what looked best, and the limitations on their subtitling equipment, and the official DVD spec just happened to end up with the same sort of solution to subs (which is why their subs haven't changed much in appearance for 20 years).
Things should be a bit better with the new formats.
From I can remember both HD-DVD and Blu-Ray allow for much more to be done with subs, but i've got a feeling it was HD-DVD that actually had the better options from the word go**.
I know blu-ray players have at least 2 specs, with some features that were standard on HD-DVD only being adopted for the newer blu-ray players and I think the PS3*, so if distributors play it safe on the compatibility front blu-ray still might have some limitations in regards to subs etc.
Oops, gone way off topic
*Due to it's nature they were able to update it's functionality.
**I beleive network connections, and picture in picture (for things like storyboards/interviews/commentaries to be shown at the same time as the main feature) were standard in V1 of the HD spec, but only adopted by the later blu-ray players.