Very bad idea as you can't switch 2 gems from one slot to another one then - which is necessary for bombing, for example. Only solution: You would have to hit whatever key for switching gems instead of doing that for combining.
Lets put it another way: Say you place a slowing gem down. Then you go to place the mana gem in an adjacent trap, and your finger slips. Oops. You just crippled your epic mana gem by combining it with the slowing gem.
You also have "u" for direct upgrade, shift+g+click and ctrl+g+click for bulk combining, and d for duplicate.
If I could combine without pressing g I don't think it would save any time. Plus with lag it's helpful to get the visual feedback of the combine icon lighting up so I actually combine instead of swap.
i create my favorit gem at the start, duplicate it a few times and put the gems into some towers. after this i only upgrade them in the towers every few waves.
my inventory is empty. then i create a bombing gem, duplicate it 35 x and start bombing. and so on ...
now if you have some gems in your inventory you want to keep for later action you still can move them to empty slots at the bottom of your inventory as bombing starts from top to bottom. only if your invetory is full this could be a problem.
i assume you use shift+b for bombing. when you have gems in your inventory you won't use for bombing you always have to be careful ....
Hit 'B' (or click with the mouse cursor) and then hold CTRL+SHIFT while clicking on your target (wave stone or critter). That works just like Astroshak described and the keys are closer together.
at the moment i don' bomb, just beating the fields on haunting difficulty. even with wizzard level 1013 some fields* are still hard and i gave up on them for now.
( * A6 and B3 at the moment, i cleared E, F, G, H, I complete so far, D and C are the next to conquer ...)