The Pokemon that you cannot get in Omega Ruby are:
The evoluntion lines of: Bulbasaur, Charmander, Squirtle, Caterpie, Spearow, Ekans, both of the Nidorans, Poliwag, Bellsprout, Shellder, Gastly, Exeggcute, Cubone, Lickitung, Mime Jr., Scyther, Jynx, Munchlax, Dratini, Sentret, Hoothoot, Ledyba, Mareep, Bonsly, Hoppip, Yanma, Wooper, Gligar, Smubbull, Sneasel, Houndour, Larvatar, Starly, Bidoof, Burmy, Combee, Buizel, Stunky, Rilou, Hippopotas, Croagunk, Snover, Patrat, Purrloin, Pansage, Pansear, Panpour, Woobat, Venipede, Solosis, Ducklett, Vanillite, Karrablast, Foongus, Ferroseed, Litwick, Shelmet, Mienfoo, Golett, Pawniard, Chespin, Fennekin, Froakie, Bunnelby, Fletchling, Scatterbug, Litleo, Flabébé, Skiddo, Pancham, Espurr, Honedge, Spritzee, Swirlix, Inkay, Helioptile, Tyrunt, Amura, Goomy, Pumpkaboo, Bergmite, Noibat, Omanyte, Lotad, Cranidos, Tirtouga, and Clauncher.
As well as: Farfetch'd, Kangaskhan, Tauros, Lapras, Articuno, Moltres, Zapdos, Mewtwo, Mew, Dunsparce, Quilfish, Shuckle, Smeargle, Miltank, Celebi, Jirachi, Pachirisu, Carnvine, Rotom, Phione, Manaphy, Darkrai, Shaymin, Arceus, Victini, Basculin, Sigilyph, Emolga, Cryogonal, Stunfisk, Heatmoar, Durant, Keldeo, Meloetta, Genesect, Furfrou, Hawlucha, Dedenne, Carbink, Xerneas, Yveltal, Zygarde, Diancie, Lugia, Sableye, Seviper, Lunatone, Kyogre, Dialga, Sawk, Thundurus, and Zekrom.
Sources:
This
and this
