1) There are somethings that Embagro can't stop a pokemon from using. Take Marowak for example. Using Embargo on it doesn't stop it from using Bonemarage, Bone club, and whatever bone attacks it has because it can't stop Marowak from using its Bone Club. In a similar manner I don't think Enbargo can just prevent Samus from using her suit. Both things are essential to their character and to their attacks.
2) Guard swap switched any CHANGES in the opponents Def and Sp.Def. Samus doesn't change or enhance her def, she just enters battle fully ready to ****. There's no additions to her def that Mewtwo can steal. You might say "Well her extra suits add def" That's about as ridiculous as saying you can steal the extra def a pokemon gets by evolving.
3) The main reason we in the end decided that Samus beat Mewtwo is that Samus is a VERY bad match up for Mewtwo. First off, Mewtwos default best attack, Psychic, is practically worthless in this fight. For damage purposes attacking Samus would be like attacking a Steel pokemon, the damage from psychic is halved (and don't try to bring up the "Mewtwo can just attack Samus inside the suit argument" Defend Order says otherwise). On top of that, Samus receives various suits that reduce the damage done to her even further (up to 75%) so essentially, Psychic ends up doing 87.5% less damage then normal.
4) Samus would have the equivalent of a high def stat. I looked through the pokemon and choose one that I felt that would have equivalent def stats to compare Mewtwos attack to. I ended up finding Magnezone, a Steel/Electric pokemon that I would estimate weighs around the same weight as Samus. He has 115 base Def and 90 base Sp. Def. Given Mewtwos not as impressive attack stat and Samus high def stat he will probably try and use a special attack. The problem here is some of the special elements are already blocked by Samus suit. She's resistant to extreme heat and extreme cold by the Varia suit which are some of the more common special elements a Mewtwo may try and pick up. She becomes resistant to Dark from the Dark suit and becomes resistant to Poison by the Hazard Shield.
Someone suggested using Earthquake to abuse the potential electric weakness but Samus can stay in the air indefinitely preventing ground attacks. She just shuts a lot of crap down
5) Whatever she doesn't end up shutting down it practically negligible due to the fact that she has multiple ways obtain temporary invincibility. She can Screw Attack, Speed Booster, Shine Spark, and use the Hyper Mode on the PED suit. The PED suit is a big one as she can take any attack and only make it end up hurting her 100 damage and become invincible for 35 secs.
6) Samus attacks are mean. The Spazer causes her attacks to penetrate all inorganic matter (which would kinda include barrier and light screen) and the plasma beam penetrates all organic matter meaning if a beam happens to hit Mewtwo there's not much he can do to resist it. Now I know the beams won't 1 shot Mewtwo as the Ice beam does about 100 damage and the Missiles do about 200 damage. While Mewtwo (before suit resistances) ends up doing like 300-500 to Samus. That 300-500 gets reduced pretty quickly while that 100 CAN'T be resisted (it's kinda like Seismic Toss, unless you have something to flat out resist the damage it does full).
7) Samus has Powerbombs and can call in a Carpet Bombing with her ship.
For reference, Samus gets hit by a hyper beam equivalent of Psychic and looses about 500 HP (out of her 2400 HP). If we are talking absolute one of the peak Samus. She then gets this power to fire right back at the enemy.