lol at Ike boards being busy. We have like, 8 people at best who go to tournaments regularly, and small number of people that plan too, but are in a bad area for tournaments/too young/don't have the money/etc, and then random people that come, ask one or two noob questions and leave. >_>
Anyhow, I have very minimal experience against Samus. Just online against a guy I only ever beat once. And that was against a character he was trying for the first time. I haven't played another Samus since, and I don't poke around this board too much, so please correct me if I get some things wrong.
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Samus is one of the few characters that can genuinely say that their projectiles affect the match-up. Unlike Luigi or Ivy where the projectile has basically no affect due to their speed and spamability, Samus has 4 projectiles, all of which that can play a roll in helping her in this match-up. I find it not dissimilar from the Link match-up, just switch the bad recovery flaw with the hard time KOing flaw, and throw in a not quite as affective close range combat ability. Ike has a tough time getting up close, but once he's up close, Samus will have a hard time getting him out of her face.
Z-air, obviously, is a saving grace for Samus in this match-up. It's one of the 4 non-projectile moves that can out range Ike's fair in the air. Use it. A lot. Particularly once he's out of optimal missile range. It will force him to either shield or dodge. However, once you're in fair range, it's usefulness with diminish somewhat.
Speaking of the missiles, they can defiantly hurt Ike's approach. Particularly the homing ones. I believe there is a way for Samus to fire off 3 of them between her 2 jumps, canceling the last one correct? Use that tech. However, be aware that a lot of Ike's attacks can cut through the missiles, cause them to go off, and leave him unharmed. If they are fired too closely together, an fair could take out the first two, and leave Ike with enough time to shield the third one. Perhaps mix it up with a super missile as the third one at ground level.
Oddly enough, I believe that bombs may cause more of a problem for Ike then the charge shot. Ike spends a lot of his time either on the ground, or SHing an aerial. Bombs can affectively block him, if only momentarily, or disrupt his attack. Anytime you aren't using a different projectile or zair, and he isn't in your face jabbing, drop one of these.
The last of Samus's projectiles, the charge shot, has it's uses alright in this match-up. It has a bit more hit-stun then her other projectiles, meaning there is a very small, but still usable, chance of another projectile that was already in motion hitting Ike during the hitstun while he's unable to dodge. As for a fully charged shot as an KOing option, I find it unlikely to occur, but plausible. Just be sure you don't fire off a fully-charged one when in counter range......
Thats quite a wall of projectiles Ike has to get through, but once he gets through, he will quickly rack up the damage on Samus. Jab Canceling everyone knows about, and just how deadly it is. A few rounds of jabs, and Ike has probably made up the damage he took getting to Samus. His throws are weak enough he can flow attacks out of them easily, Utilt and Aether hold back a lot of Samus's aerial options outside of Zair, Jab beats out her other options on the ground. That, combined with the fact Samus lacks an easy way to juggle Ike (unlike fox who has his utilt), Ike has the advantage here.
If it goes up close air-to-air combat, Ike has the advantage if he's above, below, or behind Samus, but is most likely at a disadvantage if he's in front due to that pesky Zair. Ike's Nair and Uair outlast AD's, Bair comes out frame 7, Dair is the 4th most powerful spike in the game, and Fair beats out Samus's non Zair attacks in range. Keep Ike in front of you at all times, otherwise Samus will be eating Ragnell. Ike needs to avoid being in front of Samus as much as possible, or else he will be eating Zair to the face.
In pure KOing terms, Ike has a very clear advantage. Every move except 3 of his throws can KO. Samus has some weight to help her, but Ike has better survivability. Correct me if I'm wrong, but Samus's main KOing move is Dtilt, which KO's vertically. Ike is great at surviving vertical KO attempts. One of the best in the game in fact. 5th best IIRC. Make sure you keep Dtilt fresh, because even then it's going to take a while for Dtilt to KO Ike. Samus's other options for KOing are gimping.
This is where it gets a bit more interesting. If Ike is off stage, his ability to get back really matters on a lot of factors, and one in particular: has he used his Second jump yet or not. If you start pelting him with Zair or missiles before he has used his second jump, he still has a good chance of making back. Zair and missiles simply don't knock him far enough back unless he's at very high %s. His aerial movement is on par with Toon Link's, so a small knockback while he still has his second jump isn't going to do much. During Aether, you have to hope to hit him during the peak. However, if your attack knocks him upwards (like Zair does IIRC), you just made his time a whole lot easier. Now he can quickly throw out quick draw and get the heck away from the edge of the stage while taking only a minimal amount more damage. If it knocks him backwards, it better be a good amount. While Ike has probably already used his second jump by this point, he can still move back towards the stage edge and try again. A fully charged shot would do the trick here. However, it would be easier for Samus to attempt to Dair spike him, or stage spike him with a Bair then to try to keep him back with missiles and Zair. Samus's best bet is to land a Dsmash, which can send Ike into his dead zone rather quickly, so she doesn't even have to bother with gimping. >_>
When the coin is flipped on the other end, Ike does have some methods of gimping Samus. I've found Dtilt to work better on Samus's Up B then a lot of other Up Bs. Same idea with Eruption and Dair. However, Samus also has her grapple to grab the ledge with. This can work, and is probably the best option for Samus. Just be aware there is still danger in doing this. Ike can fall down the grapple line and throw out a Dair in an attempt to spike Samus while she's still hanging. When recovering as Samus, take the time to throw out a missile or Zair to knock Ike back long enough to grab the ledge.
Overall, I feel that the match-up is 6-4 Ike's Advantage. Again, comparing it to the Link match up (which is around 5-5), Ike has a hard time getting to attack range, but once he's inside Samus has a harder time getting Ike out then Link does and a harder time ranking up damage outside of projectiles, combined with the fact she has a harder time KOing Ike then Link does.
For stages, Samus should shoot for FD. No way for Ike to use platforms to avoid some of the projectiles, or to use his own set ups with the platforms. Ike will probably be aiming for BF for his neutral pick. For CPs, Jungle Japes is always a good CP against Ike. Ike fails there, hard. Outside of that stage, it really depends on the Ike's playing style. Some Ikes even like RC as a CP stage. However, Samus should defiantly strike Pirate Ship. It's Ike's best stage by far. Ike has his water spikes (Aether -> Dair works like a charm), aether sliding, wall infinities, low gravity for his AD eating aerials, good platform spacing, it has everything for Ike. Worse of all (in Samus's prospective), you can't really gimp him outside of landing a spike yourself.
I think I covered it all....