Well, after 4 hours of playing IRL last night, if matchups where up to us (which of course they aren't we're only two people.), it would look like this:
Ike vs. Squirtle - Yeah, I could safely say this is a 35 - 65 advantage Ike at worse case scenario, and best case would still be like 45 - 55 advantage Ike. Speed and mobility did not help IRL do anything majorly with me when I used my fast attacks, also the poor thing is too easy to kill. The one thing I found troublesome wast he HUGE knockback d-throw had on me, it even killed me a few times when I was high in the numbers
Ike vs Ivysaur - Kind of questionable, but I think it could be something like 40 - 60 advantage Ike, or it would even make Ivysaur in the favorable somewhere at 55 - 45 position depending on some factors, so I am going to say it can be sligtly neutral? Razor leaf was way too easy to powershield. Bullet Seed can be a nuisance but will only do about 20-30% damage if you DI out of it, and if it misses dear God how you are going to pay for it. Bair was alright for stopping any ground approaches but did that stop me from using my aerial game to counter? The answer is not really, not unless you fullhop it and if necessary retreated/assaulted with the bair. Ivysaur is too easy to ledgecamp gaurd it's not even funny. If Ivysaur tried to do any kind of gimp it would not have any result/would even end up in getting you killed, and that's with Ike in the unfavorable position, now put Ivysaur in the same place and just abuse the ledge invincibility frames. Razor Leaf would go right through Ike, and if performed correctly you can double jump to grab the ledge again and refresh the invincibility frames to make sure Ivysaur won't take you down with it when it tries to Vine Whip Tether recover.
Edit: I fought Onxy, and what he did different compared to IRL's Ivysaur was instead of chasing me offstage which I don't recommand doing unless you're going to Razor Leaf Ike to try and steal his second jump, he would sit at one spot at the edge and just wait for me to get up, and it worked numbers because he would use Vine whip if I tried to jump recover or the same results if I tried to roll, Vine whip has some good hitboxes I must admit. He could've also simpleydo a ftilt/Fsmash/grab if I just crawled back onto the stage, with this it puts Ike in a very unfavorable place if he is hanging on the ledge. Other than that I did the same stuff that I would've done if it were IRL's Ivysaur, and although Onxy probably doesn't like the wifi, I'm sure I wouldn't have won some of those matches had it been in person (in fact he even won one of them). So with that done I would give Ivysaur / Ike a Neutral matchup at worst, and possibly a 60 / 40 advantage Ivysaur at best case scenario.
Finally...
Ike vs. Charizard - Charizard has from a 60 - 40 advantage to a smaller advantage down to 55 - 45, maybe it could be neutral, but for me I found Charizard to be the most difficult of the three. Flamethrower is a great tool to use, it would force me to try for an aerial approach if I didn't get caught in the flames, and if I did would either force me to DI back, or go for an Aether escape as a gamble which would either end up with giving me some breathing space, or would end up being punished with a strong attack or a throw. Not something to use for a very long time thoguh or Ike will pick up on it and just charge a Quickdraw which can be held forever until eventually Famethrower dies down. Rock smash is another good thing to use, not only to rack up damage, but to possibly score a kill, the sweetspotted Rock Smash has some VERY nice damage and knockback, and even when it wasn't swettspotted would really limit from frontal assault due to the amazing range it has. Charizards throws are great, compared to Ike it's used for the same reasons: to get your opponent off the stage. Even Charizard's dthrow can be used to score some stocks, keep it refreshed as much as possible by pummeling Ike when you have him in grab range and/or using another kind of throw when you know Ike won't die from Dthrow alone. Offstage is the last place Ike wants to be when recovering, one hit is all that's stopping us from getting back onto the stage and death. Charizard's recovery is very great for gimping Ike and coming back to the stage. If Ike is using Fairs/Bairs to push you back further offstage just pick up on it and simply airdodge, a smart Ike won't be using Nair as an offstage gaurd because it has too much lag in the air, but don't get confused, he could just as well stay near the stage and use this to push you up and away for some extra damage. Whatever you don't let Ike dair spike you or you are dead no matter what. Finally if you're feeling confident you can fake-out Ike and do a glide recovery to the other side of the stage if they aren't expecting this, however if they catch on to this you're betetr off just getting back on if possible...Finally use your smashes accordingly, you will probably have to be like Ike and only use them when you know they will hit, because that's good when it connects but if you miss you might regret it.
Edit: Maybe for Charizard if you play your cards right you can get 65 - 35 advantage Charizard.
When put together, I think Ike is at a slight advantage, it's up to you to come up with a number for that, but Ivysaur and Charizard can beu used to keep the matchup even if not putting you in a good place, as for Squirtle...really all hope is lost for that tiny thing... For counterpicks I would recommand anything that is Jungle Japes (Ike has a bad recoery, the rushing tide doesn't make this any better), Norfair (this gives you more room to work with), Luigi's Mansion (when the place isn't destroyed, this limits Ike's options and only benefits you're ranged game), Frigate Orpheon (The first stage doesn't have a ledge on the left side, so Ike WILL have to land on it with Aether which leaves a lot of room for punishment, but this also doesn't help you recover either, CP this at your own risk), and Castle Siege (The first stage is small, so that puts Ivysaur and Charizard in a good place, the second stage has a lot of room to give Squirlte a fighting chance, and the third stage is great for messing up Ike's placing due to the careening stage.)
Again, if any other PT's want to Wifi me feel free to leave a PM or a profile message, maybe with experience on a different PT I may change this post accordingly, or just further prove what I've said here true.