Always nice to see some decent HGSS hacks. Good luck! If I get some free time, which I can't really promise, I'll see if I can help you with those items. I've been doing some disassemblies for DP and HGSS recently and am pretty familiar with the area.
Also, you could just temporarily delete the ORAS/XY patches when you are using the web exploit. Go to your 3DS's Data settings and remove the Extra content for Pokemon in there.
Well, the Pokemon don't have full bodies, so even if it were transparent, there would just be a giant hole.
As you can see in the backsprites here: http://pokemondb.net/sprites/crobat
They don't and will not. We had exploited their services to allow Powersaves to work with PKHeX for like two days and then they immediately blocked us from doing so.
Have you tried playing this ROM hack yet? It's 90% of what you are looking for: http://projectpokemon.org/forums/showthread.php?27285-Cynthia-B-amp-W2-Hero-Sprite-Replacer
Update on what? Nintendo is not going to un-fix their systems for us. It could takes a few months or longer for another exploit to be released. It did take years to get to this point after all. Plenty of people have a decent exploit to work with now, so there is no big rush to get another one.
Did you make any script changes? If not, dump an original copy of the game and copy it's a/0/1/2 (script file) into your ROM hack. It is likely that that file got corrupted while making encounter changes.
You might be able to ask the developer of this program: http://projectpokemon.org/forums/showthread.php?44994-Mass-Editor-for-all-PKHeX-supported-files
It is impossible to use PKHeX with Powersaves. The Powersaves software does not allow for arbitrary save edits, which PKHeX is built upon. Powersaves only allows for a small subset of codes which their servers provide.
These are just giant groups of bots. I've done what I can to prevent it and the notices you have all received are an indicator that the forums did in fact stop them in their tracks.
The information on the official site is not up to date (It doesn't even list the main Pokemon games). Unfortunately, there is no easy way for you to back up your save.
There are a couple of other impossible cases, such as having a HA parent that has not had its HA released. Or a male-only species like Tyrogue getting egg moves passed down to it from outside of its evolutionary tree.
When you open up system settings, does it still say 9.5.0-22? There are a couple of external factors that can cause it to update, so check that first.
Does the browser still crash?
For which games? If it's Gen V or below, it will affect it because of how the seeding advances and would skip the set nature.
I will also be moving this to the Pokemon Legality subforums.