Aggron with T-Bolt?? Its Base SAtk is only 60, its Base SDef is only 60, and its Spd is only 50. What that means is your Aggron will first have to eat a Water attack since most Water-types you will face will be faster, and then have to deal with the fact that an Aggron T-Bolt will not be a OHKO either. Just a bad choice. Gardevoir, on the other hand, can not only learn T-Bold, but Calm Mind as well. Throw in the fact that it has a Base SATk of 125 and it can handle all Water-types, not to mention Flying-types.
Swampert also outclasses Blaziken in about every single way. MUCH better typing, with just one weakness that Ice Beam can generally handle. Its Base stats are better spread, allowing it to take hits while Blaziken is quite fragile. It can learn its moveset long before you reach the "elite" 4, while Blaziken isn't even able to learn its best moveset in RS. A STAB Surf and STAB Earthquake are a deadly combination, and much more effective than STAB Flamethrower and STAB Sky Uppercut.
To be honest, Swampert and Gardevoir are good enough to roll through the game by themselves. You don't even need a third. Hell, Swampert can do it by itself without having to level up as high as other Pokemon do for a solo run.
Still, you asked for the BEST 3-man team, so I refer you back to my original post.
As for your edit, if I am understanding you correctly, you are wanting to know if a team of Blastoise and Raichu have any weaknesses? The short answer is no. I would suggest giving Raichu Substitute and Focus Punch though, and make sure Blastoise has both Ice Beam and Earthquake. That will ensure that you can do at least normal damage to every type that you will see in the game. Substitute comes in very handy since you are pretty weak on the special side. Well, Raichu is weak defensively in general, but you get the idea.