First off, unown's slot isn't TOO hard to edit around, from what I know. it's just somewhat tedious. (you'll need to insert the same sprite for every unown form, plus a menu icon for each one as well.) I have alice's alt form in unown's slot in my hack and she works fairly fine. Spinda's slot mainly glitches up with the color pallet. I believe I put CIchirin here, but it is pretty noticeable on her. (her nun robes have random red splotches on it.)
Secondly, I know there is a fix to deoxys and mew's obeyment patterns. (here's for mew:
http://www.pokecommunity.com/archive/index.php/t-235854.html ; colcolstyles has the correct hex edits you'll need to make). However, deoxys is another can of worms entirely. From what I know, its stats are hard-coded, with the exception of HP, so you can't really edit deoxys without a LOT of knowledge.
About the overworld locations, you CAN set other mons to be in the snorlax spot. FR 1.8 has chibi yukari there, which is in clefairy's slot. This can be done via script editing in AM (or through hex)
Fossils also work normally in the wild. no fuss there. if you want to have another puppet be revived, I think that's also some scripting work.
And I don't think moving the dex numbers really messes with stuff outside of the dex itself.