Unfortunatly, Samus is one of, heck im going to say THE best character in the game when it comes to recovering. Bombs, grapple beam, Recovery, her heaviness and air movement/floatiness makes her SOO hard to clear on alot of stages.
With bombs, its really hard to edgeguard Samus, esspecially with Marth, who has no projectile. Your best bet would be just to wait until your friend is done with all his fancy samus recovering and try and launch an attack when he's just getting back up onto the stage. Either that, or dtilt'ing is good for a Samus who likes to get back on the stage from underneath. Sometimes, just a shorthopped forward air can mess her up, if she's that high up.
Marth is at a little bit of a disadvantage against Samus, but popping her up in the air is your best bet, uptiliting and uair own Samus. Exploit her floatiness and your range in the air.
it is hard to fight her in the fashion Marth would tear anyone else to shreds. The most prominent aspect of this thesis is seen in Samus's playing style: Where Marth is most effectively played as a precise-hitting, sweet-spot exploiter, Samus is messy, mushy and ALL OVER THE PLACE. Her firey attacks (bombs...?), explosions, and huge span of range all help to rack up that damage %. The saddest thing is this is how I've seen all Samus players purposefully act, and it tears my heart to peices to lose in a flaming, smoldering state.
The wrong thing to do would be to fight Samus in the same way the Marth would fight anyone else. Of course, every other character requires some sort of slight alteration in approach, but still, treat Samus as an extreme. THE alteration I've found to make versus Samus is to play carefully--even more careful than you would be versus any other character. Her bombs, missiles, and Big Friggin' Gun are all moves that she can use to get in the way of your playing, and make room for an approach to grab or shoulder slam you. So, in light, beware.
Here are the things I consider most when playing Samus:
1. Play CAREFULLY: Being her messy self, your Samus-playing nemesis would love to see you screw up a silly wave-dash and be blown into oblivion. No fancy tricks unless you are SURE that the outcome will be what you expect.
2. COUNTERING: I'm sure you know this one, but sometimes people foget in the heat of a passionate battle. Marth's Counter does NOT reflect projectiles. When playing Samus, don't use it to fiend off nasty missles, bombs, and blasts. A simple tap on the L button will do for all the defense you need versus most of that stuff.
3. STAY OUT OF THE WAY: Samus, as I said, is messy and all over the stage. Don't ever blindly rush in to attack--be defensive! An orange pinball dropping bombs at a rate of more than two booms per second is NOT the best field of battle for Marth! When she blows her projectiles at you, jumping over them is a good tactic. Just wait for your chance to strike--it will come.
4. DODGING: Marth has an excellent dodging roll (L+Foward or Backward); when playing Samus (who, by the way, has the broadest shoulders in the game, as a female), don't be timid to roll away. This is one of those simpler tactics turned strategic--abuse, abuse, abuse! Considering Samus's slow Charge Shot, slow charging footspeed, slow-dropping bombs, and (well, actually painfully dangerous) missiles, there are always opprotunities to roll dodge. This is far less hazardous than trying to wave-dash through her projectiles or simply stay put and dodge (L+Down). Be careful, though.
5. AERIAL: Keep away from overdoing your aerial moves. Samus underneath is not something to see as an easy striking opportunity. You should know why. However, being in the air is a great place to parry Samus's lesser projectiles with the extensive reach of Marth's Foward+A and Backward+A slashes. Also, a shffl'd Foward+A, Neutral A, or Down+A are excellent ways to offensively attack. Don't become predictable, though.
That about sums up the problems that I've ever had playing Samus. As far as Edge-guarding goes, Samus has the best recovery in the game. Don't waste your breath worrying about finding some way to keep her off; finish her off slowly. That will have to be done to some character...might as well be Samus.
Sorry so long of a post. That's all I have for you.