The thing that I have always maintained when working with teams is to make sure that you are working towards countering your own weaknesses and utilizing your opponents'. That being said, you still have Flannery, Norman, Winona, Tate/Liza, and Juan to beat (not even counting Trainers along the way) before you can challenge the E4.
So if you build just a team of 6 Pokemon to use throughout the whole game, make sure that their movesets compensate to the point where you have a plan for every major battle (heck, even minor ones because the Walkthroughs include Trainer data in most cases).
Now you want my recommendations, and before I go on that list, use Pokemon that you enjoy working with. Regardless of what anyone else says, if you want to use a Swellow, go for it! (True, Beautifly isn't the best, and neither is Swellow...)
However, here are some general ideas for you to consider (and yes, there are more than six I know...) [Sorry I didn't check on availability beforehand, I'm lazy...  ]
Swampert
Absolutely bomb in those games, and in the best way possible. Especially if you do a varied moveset, this will be a great choice, so keep it.
Manectric
Great for double battles, although not too many of those happen in the game that are from the "higher-ups" (Tate/Liza the obvious exception, but it won't help against their Rock types).
Camerupt
Other than the fact that you already have Swampert, I would definitely consider this one as a nice possibility (never pull it out on a Water type!)
Sableye
Aside from the fact that it has no weaknesses, Sableye can be a bit of a liability in battle (also availability might be an issue), but consider it.
Dragon/Flying
Yes, I'm leaving that one open, because it depends on what kind of player you are. Like Attack? Go Salamence, but Altaria is a great alternative and perhaps a little easier to get (not necessarily train).
Gardevoir
As JsXtm said, great Special Sweeper, especially if you still need one on your team. Another viable Psychic option might be to consider a Medicham.
Ludicolo
If you really don't want to keep Swampert, this is probably the best Water-type besides it introduced in this Gen. (Free to argue if you wish.) Again, varied moveset helps extremely here.
Metagross
Another great Special Sweeper if you don't like having Gardevoir. A lot harder to train, out of experience.
Kecleon
Admittedly, this one is a personal favorite due to its ability (just plan to be the first to strike and faint the opponent otherwise they might counter well.)
Hope this gives you some ideas! Welcome to Psypoke.
AEPMT   
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for team, i prefer those pokemon with 2 really high stats, preferably over 350 at level 100 (e.g. hp & attack for blaziken), alakazam will do great as special sweeper, golem a tank (as you can get these 2 very early in the game), i basically chooses the ones with best stats. (check the psydex for the stats)
