So after looking through GW (Still haven't played it) these are the differences I've noticed:
1. Character generation is different.
No race/class breakup class/race consists of two randomly (or not randomly or partially randomly however you choose) selected elements... Yeti/Bat Swarm. or Hypercognitive/Hawkoid , or Radioactive/Plant
The game suggests keeping combinations that would be "silly" and think up a way to explain it. (IE a rock/hawkoid could be a gargoyle.)
The powers come from your types.
There aren't any feats. Instead random mutations seem to kind of take their place.
This is where the cards come in. They change periodically, so the cards function as sort of rolling on a random table.
Stats- you put an 18 in your Primary type's stat- and a 16 in your secondary type's stat, then roll 3d6 for the rest.
2. Weapons and Armor are different (sort of)
Instead of specific weapons or armor, they have general "categories."
Light or Heavy armor and shields. Each gives a specific bonus. It's up to the player/group to describe exactly what it is or looks like.
Same with weapons, Light one handed, light one handed gun, heavy two handed gun... Etc...
Cards also come in here as well... Omega Tech seems to function as the magic items of GW. They're unstable though so they tend to come and go, unless you salvage them, in which case the remain, but at a reduced power level.
3. Skills are the same but different.
The skills work pretty much the same as in the rest of 4e, but some skills are swapped out for ones that are more appropriate. No Arcane skill for instance, but Mechanics is a skill, or Conspiracy...
Your two types plus a random roll determine skills you are trained in.
4. XP totals are different. Way different.
10,000 xp gets you to 10th level in GW. This is also the highest level the game goes to... Not sure if the expansion sets comming out will go to higher levels... Since there are two more though- it seems reasonable that the next one will be paragon level, the next epic... But I have no real idea.
All that said, combat works the same- as does everything else in how the game is played at the table. Monsters are exactly the same but with added keywords... It even suggests taking monsters from D&D for use in GW.
So... theoretically I think the two types of characters could exist side by side, and not have an issue. BUT- swapping stuff between the two would take some House Ruling...
Adding random mutations to D&D characters would probably overpower them- and since weapons/armor are kind of different a GW character using D&D style items would be awkward...
Not sure by how much though- someone actually good at math could tell you better then I could.
Also the D&D character would advance way slower then the GW character.
It would be interesting to play around with some house ruled mish-mashing though.
I think it might be fun to throw in some random mutations in a D&D game too if you were doing like a far-realms adventure or something- or the let your players find some omega tech D&D meets Blackmore spaceship style... With no salvage chance maybe?
Because GW is a chimera of card game and rpg, I don't know how it would work. It depends if you want to take Amethyst into GW or GW into Amethyst.
Not really- the cards function more o less as a random table you roll on would, and make it easier to track what mutations/items you have currently.
Kind of like if you combined the current power cards with a random table.
There aren't any card game mechanics involved- you're not like comparing cards vrs the DM or something.