When I first played through saphire, if I remember correctly I used:
Swampert, Aggron, Armaldo, Exploud, Sharpedo and Kyogre. Not a very balanced team, but I loved each of my choices.
This time round, I'll be going for different teams on both OR and AS.
Ruby:
Sceptile - Love his new mega, dragon is a favourite type of mine and sceptile has always been a favourite starter of mine to playthrough with.
Mawile - As I had saphire and my brother had ruby, I never used mawile. I still have never used it, despite the craze in XY. There have always been other steel types which appeal to me more, but I'd like to give it a shot woth it's new fairy typing.
Gallade - Obviously never used it in gen three. Used gardevoir in my X playthrough, and she was great. Honestly always hated Gallades type and design, so didn't pick him up in any other gen. But it's mega is alright, so again I'm wanting to give a less loved pokemon a chance on my team.
Armaldo - Loved this guy in saphire, but never used it to it's potential really. Knowing now that bug is super effective against the ever present grass, psychic and dark types In hoen I'll be taking him along again.
Milotic - Again never used her before. Nightmare to obtain until BW, never actualy had one till then (where WIFI allowed meto complete a national dex for the first time). Her design has grown on me in the past few years, and I now appreciate the use of bulky pokemon better than I used to. Was all about damage output.
Camerupt/Groudon - briefly used camerupt but fell out of love woth it quickly. Was always disappointed with the lack of fire types in hoen, still am really. But now that groudon atlast gains a secondary fire typing, I'll be giving camerupt a go and if he sucks as bad as he looks, I'll just swap him out late game for the big guy.
Saphire:
Swampert - Favourite of the gen three starters. Have had Atleast five swamperts in my time, ground water is one of my favorite type combos to use in game. Swampert has always been a beast, and his new mega just looks like a dream. Can't wait to get running this guy in the rain!
Heracross - Once again, never used this guy. Like armaldo I'd never really appreciated the use of bug types, and fighting type is nice too (despite the birds). If indeed he is available mid game, he'll be making the team.
Metagross - Hated this pokemon until gen six really, and he's only just grown on me. As he's being given away though I'll take him along, making the most of the oppertunuty to have him from the start of the game rather than having to wait right til the end to then painfully train a beldum. Awsome pokemon statistically, so I'll save one to train properly for online and use the second to have some playthrough fun

Craydilly - My brother chose craydilly an I chose armaldo, so I'm wanting to give him a go

there's a chance I'll go for ludicolo instead, though with swampert I'll have two water types which I'm trying to avoid, and itl leave my team lacking one of my favourite types. Rock.
Glalie - Mega glalie? Yes please. Amazed at finding this rather lack luster pokemon to be one of my favourite megas so far from all of gen 6. Love his design, and the one in my demo is adamant which is a bonus

Altaria/Rayquaza - Love dragons and am making it a personal target to have one of every fully evolved dragon trained up from playthroughs

never liked her as she seemed too ' girly ' when I was younger. My bro had a level100 altaria he trained in colluseum and he still today stands by her being awsome. So I'll give her a space on my team. Similar to camerupt, if I don't like her I'll just swap her out for a shiny EV trained rayquaza I have.
So that's basically it. Have true I make two balanced teams, utilising pokemon ie never use before or have but have not really appreciate due I being about ten when these games came out.
I tend to keep one version with it's original file, but play over on the other. I'll most likely keep rubies save file so I can try out a water monotype or rain team with primal kyogre on saphire!