Do you still own the 3DS? that might well be the best console to play all the games on.
3DS:
GEN 1 is officially on the Eshop, the games support trading via WiFi
GEN 2 will be on the Eshop September 22nd, these will also support trading via WiFi. Unofficial CIA's exist which support WiFi trading however.
(You can import your Pokemon up to GEN 7 if playing the official Eshop releases of GEN 1 and 2)
GEN 3 is possible to play on the 3DS with custom built CIA's, you wouldn't be able to trade though unless you dumped your save and used an emulator on the PC to trade, then restored the save to the 3DS after.
GEN 4 and 5 can be played on the 3DS with a cheap $10 flashcard, although i'd say spend $20 and get a good flashcard if your going to invest in one.
GEN 6 and 7 are obviously 3DS games
So as you can see it is possible to play every Pokemon GEN on the 3DS, with full trading / link support with the exception of GEN 3.
Windows:
TGB Dual for GEN 1-2 (Supports link cable emulation)
VBA-M for GEN 3 (Supports link cable emulation) This will also play GB / GBC colour games, however i found the link cable emulation to be quite buggy so i'd recommend TGB Dual.
DeSmuME for GEN 4 to 5, this can link to GBA games, however does not support WiFi emulation, meaning you can't trade.
melonDS for GEN 4 to 5, this emulator is pretty new and requires quite a powerful PC, however does support WiFi emulation, so in theory trading should be possible. I've not tested this however.
Citra for GEN 6 and 7, requires a powerful PC, no WiFi emulation so i'd stick to your 3DS for GEN 6 - 7
I hope that's some help!
If you can spare the cash at some point I think it's well worth investing in the physical copies of Pokemon games, i've gradually purchased all the core games over the years. Some we're going pretty cheap, for example I got sealed copies of Black / White and Black / White 2 for £7 each. On the other hand Heart Gold / Soul Silver are going for £50 used here which is crazy.