Eeveelutions (I think this one would be rather interesting AND you can technically have each Eeveelution as early as Level 2 so you can train them us as you normally would a Starter and early caught wild Pokemon)
Fossil Pokemon (Another interesting idea. Sure they'll all be Rock-types but that would be part of the challenge, especially in games which have a Grass- and Fighting-type Gym Leader/Elite Four (and also Water- and Steel-types to an extent))
Pikaclones (Pikachu family, Plusle, Minun, Pachirisu, Emolga, Dedenne. MAYBE Marill if you want to stretch it)(Another interesting one that may be even more limiting and challenging if there's a Ground-type Gym Leader/Elite Four)
No Evolutions (Farfetch'd, Kangaskhan, Pinsir, Tauros, Lapras, Ditto, Aerodactyl, Unown, Girafarig, Dunsparce, Qwilfish, Shuckle, Heracross, Corsola, Delibird, Skarmory, Stantler, Smeargle, Miltank, Sableye, Mawile, Plusle, Minun, Volbeat, Illumise, Torkoal, Spinda, Zangoose, Seviper, Lunatone, Solrock, Castform, Kecleon, Tropius, Absol, Relicanth, Luvdisc, Pachirisu, Chatot, Spiritomb, Carnivine, Rotom, Audino, Throh, Sawk, Basculin, Maractus, Sigilyph, Emolga, Alomomola, Cryogonal, Stunfisk, Druddigon, Bouffalant, Heatmor, Durant, Furfrou, Hawlucha, Dedenne, Carbink, Klefki)(Looking at the list maybe you should limit the list by only using Pokemon with no evolutions in that game's Regional Dex (which maybe even add in some Pokemon that didn't have an evolution at that time). Eitherway could be interesting to see how a Pokemon that doesn't change appearance and general stat wise grows stronger and becomes better and better at its role)
Middle Stage (Ivysaur, Charmeleon, Wartortle, Metapod, Kakuna, Pidgeotto, Nidorina, Nidorino, Gloom, Poliwhirl, Kadabra, Machoke, Weepinbell, Gravaler, Haunter, Dragonair, Bayleef, Quilava, Croconaw, Golbat, Pikachu, Clefairy, Jigglypuff, Flaaffy, Skiploom, Seadra, Pupitar, Grovyle, Combusken, Marshtomp, Silcoon, Cascoon, Lombre, Nuzleaf, Kirlia, Vigoroth, Loudred, Marill, Lairon, Vibrava, Sealeo, Shelgon, Metang, Grotle, Monferno, Prinplup, Staravia, Luxio, Roselia, Gible, Magneton, Rhydon, Electabuzz, Magmar, Togetic, Piloswine, Porygon2, Dusclops, Servine, Pignite, Dewott, Herdier, Tranquill, Boldore, Gurdurr, Palpitoad, Swadloon, Whirlipede, Krokorok, Gothorita, Duosion, Vanillish, Klang, Eelektrik, Lampent, Fraxure, Zweilous, Quilladin, Braixen, Frogadier, Fletchinder, Spewpa, Floetta, Doublade, Sliggoo)(If you're wondering why I have some Pokemon out of order I ordered them when they became a mid evolution. Also, like the previous group, you may want to do this with the Regional Dex but that may remove some Pokemon available who weren't a mid stage by that point. Anyway, an often overlooked and some may even say underappreciated group of Pokemon it would be interesting to experience what these Pokemon have to fully offer)
Gimmick (Ditto, Unwon, Wobbuffet family, Power Trick Shuckle, Present Delibird, Smeargle, Slakoth/Slaking, Shedinja, Normalize Skitty, Castform, Kecleon, Order move Vespiquen, Sunny Day Cherrim, Rotom, Zen Mode Darmanitan, Yamask family, Archen family, Zorua family, Protean Greninja, Meowstic, Aegislash, Inkay family, Metronome user, Nature Power user, Secret Power user)(Now what counts as a gimmick may vary but I consider it having Signature Moves or/and Abilities which would greatly effect the way you play them be it by design or choice. Sure a lot more Pokemon could fall under that rule but I consider the ones I mentioned the most notable. I don't think I need to explain why this idea is interesting)
Pseudo Legendary (You could also add in Pokemon who's level of evolution is abnormally high. Anyway the idea here would be to see how a Pokemon who take a long time to fully evolve gets there and when they do watch them dominate)
Early Bug (Caterpie fam, Weedle fam, Ledyba fam, Spinarak fam, Wurmple fam, Kricketot fam, Burmy fam, Sewaddle fam, Scatterbug fam)
Early Bird (Pidgey fam, Spearow fam, Hoothoot fam, Taillow fam, Wingull fam, Starly fam, Pidove fam, Fletchling fam)
Early Rodent (Rattata fam, Sentret fam, Zigzagoon fam, Bidoof fan, Patrat fam, Bunnelby fam)
Canine (Growlith fam, Snubbull fam, Houndour fam, Smeargle, Poochyena fam, Electrike fam, Riolu fam, Lillipup fam, Furfrou)
Feline (Meowth fam, Skitty fam, Absol, Shinx fam, Glameow fam, Purrloin fam, Litleo fam, Espurr fam)
Pokemon Traits (
Egg Group,
Color,
Body Style)
Admittedly these are very simple theme, but hey, if you have an idea for a theme here's
the National Dex.