Speaking from the perspective of a Samus main with reasonable knowledge about Ike, I would like to express my personal distaste for this match up. Ike is just far too well suited to deal with the spacing that Samus needs to thrive.
Basically, you've got a massive sword. Samus has a history of disliking those, especially with her recent nerfs to Zair which basically removed any sort of outspacing against the FE characters. That big sword you've got, that thing kicks like a mule. Any time Samus gets hit, she may as well have kissed the front of a semi-truck plowing down the freeway at 90MPH. Samus has a history of disliking getting hit that hard (**** you, Ganon). You've got an incredible grab game and enough aerial range to follow up on throws all the way to mid-percents. That's a huge deal. Honestly, you've got no idea how big that is in any MU against Samus. If you can confirm off of a throw, you're gonna be having a great time.
Samus is inherently campy, and she likes her space. Ike is inherently rude and butts into peoples personal space. He does so through the use of his quick draw. Quick draw approaches are very scary to deal with. You've got the option to grab me if I shield, hit me if I'm landing or throwing out a move, bait stuff out of me and then WD back or in place and then punish, etc. Not to mention the tech chase game is godlike.
Issues that I see Ike having against Samus. If you don't have good platform movement and you don't inherently understand how to combat missile play, you're gonna struggle a lot. You've got to play with a lot of wavelands and you need to understand that you can approach through missiles with neutral air and close the gap. Sometimes, you can abuse the hitlag of a missile and just forward air through it and wreck Samus' ****. If you quickdraw stupidly, or are heavily reliant on it (that's pretty much like 80% of Ike mains, tbh), Samus can just lay bombs and really force you to do stuff that you don't want to be doing in the neutral game. Beware the crawl attack, btw, because that's got decent range and has actual follow ups. I'm pretty sure Ike can grab Samus out of crawl, so it shouldn't be too much of a problem once you familiarize yourself with it.
As far as tether mechanics in 3.5 go, Ike should be a pretty happy ranger with how his interactions play out with Samus at the ledge. Step 1: hit the Samus. : : Step 2: grab the ledge. : : Step 3: patiently wait and laugh as the feeble Samus struggles to get back to the stage : : Step 4: either drop ledge and bair, or just wait for the forced get up and punish the 50 frames of end lag.
But seriously, you've still got a huge sword, don't be afraid to exercise that things range and try to mess us up late in our recovery. Nair through a bomb and hit us, and all we can do is DI up and try again, if we don't die off the side blast zone.
Edge guarding Ike is relatively easy for Samus (but still scary af), because we can just up-tilt, DAFT, or backwards crawl to ledge hog while outranging or just avoiding that dumb UpB. Obviously, you should try to sweetspot the ledge to avoid getting hit, but pulling out a wall jump and going a bit high can catch us off guard and get you onto stage.
Also, we like to ban GHZ. Ike should be taking us to small stages. Aim for GHZ and WW before going to YS, because we can missile cancel on YS (also on WW, but WW is still better for Ike). Avoid DL, FoD, FD, and kind of smashville. The last two on there depend on the type of Samus. A lot of times, Samus can force you to waste your jumps with well placed missiles and charge shots, and then close the gap and start up a string. If you're playing against a dumb Samus who doesn't appreciate the zoning potential of missiles, and just spams MC, you can take them to a flat stage and have an incredible time pushing in their feces.