I missed this in the flood of 5 million posts. This thread has been more active than it usually is the past day or so.
Anyway, to actually talk about counterstrategies, here's what I've been doing, and what I'm going to do (I've played a few Villagers with this setup already), or rather, an outlook for some of the characters that I play (warning that there's some rambling here while I sort out my thoughts):
doesn't care about the Trip Sapling. As you guys saw, he can tjolt camp. Additionally, one thing that Jtails did not take advantage of was Quick Attack. It can allow Pikachu to get in when the Trip Sapling is poorly placed or Villager is too far from it, and then Villager has to roll around or trudge back to the sapling. Villager's mobility is really bad, and his grab is even worse, so getting in does a lot. Pikachu's f-smash is disjointed and can hit across the sapling without Pikachu tripping. Heavy Skull Bash is also fantastic here, as you can burst a Villager who misses his f-air or b-air for the KO at high percents if he jumps into the air. Ledge trumping Villager leaves Pikachu with lots of options because of his ledge getup time, and if the sapling is right there next to the stage, then Pikachu can grab the ledge by Quick Attacking over it, so the sapling pretty much does not have any adverse effect on Pikachu's gameplan, overall. His grounded normals don't work as well as they do usually, but SH f-air and SH d-air are as strong as ever. Ballons are a little trickier, but Tjolts + Quick Attack can save the day there too. I think EBT Villager is slightly easier to gimp than normal Villager, actually. Villager is so slow on his way up. Thundering the balloons is easier than ever, though it won't gimp him outright (it's just nice to land to get the lead, since getting the lead is what matters against customs Villager in most cases).
is one that I haven't tried, but she also doesn't care about Trip Sapling too much I think. Penetrating Needles are really good, and her f-air is good enough to poke around the edge of the sapling (it's like a small sword swing). Offstage, angled needles can pop Villager's balloons safely, but I don't know that it can gimp (I haven't tried to pop both; probably works?). Not much more to say about this MU. I'd literally just camp needles if it ever came down to it. Even if I lost the lead, I'd get it back eventually just doing this, unless I lost it by a lot, in which case the game's probably over.
This is extremely free. Well, to some extent. A good Villager can still be trouble. But FLUDD and Gust Cape push Villager away from the ledge without any risk for Mario. Fireball zoning is effective along with Cape to reflect Villager's own projectiles once Mario has the lead. If Scalding FLUDD is taken, then Mario can get that lead pretty quickly with a few uses of that and his generally good aerial mobility, and then he can just sit back and Cape things for the rest of the match. Scalding FLUDD can also pop the explosive balloons without any risk to Mario. Super Jump Punch's semi-invincibility actually makes SJP'ing Villager as he's recovering with his slow balloon trip a possibility, but it won't gimp him outright, it's just pretty disruptive to his strategy. I still wouldn't recommend doing anything to Villager offstage, though, unless Mario loses the lead. With a lost lead you pretty much have to play riskily offstage, but the amount of risk you're taking vs. the amount of risk Villager is taking is not too bad. It's about 50:50 of you getting hit by balloons and Villager getting hit by your attacks or getting gimped outright. So yeah. Villager in the lead? 50:50. Mario in the lead? 60:40. I think Mario wins overall. It's definitely not Mario's usual gameplan, but a little adaptation does actually work wonders here.
I do play a lot of Sonic, on and off, because I think customs Sonic is really strong. Hammer Spindash is my move of choice here, but it's hard, I've had the sapling mess me up a lot while trying to get to Villager using HSD. The other two Spindashes are not as useful in this MU, I find. Burning's small hop is OK for getting over the sapling quickly, but I've timed this wrong many times. Anyway, so Sonic is the master of timing people out because of his ground speed, so this one is all about playing super defensively when Villager has the sapling up, and then playing aggressively when he doesn't. At least, that's been my approach. I don't know what other Sonics are doing. I find that Sonic has no answer to the ledge camping that Villager likes to do, or at least no answer where the risk:reward ratio is decent, so I just wait out the sapling and then try again. Losing the lead as Sonic in this MU is really painful, but Villager generally has a hard time getting Sonic away from him once Sonic is in, so these brief seconds where the sapling is down is all Sonic really needs to make sure that he doesn't lose the lead. He's so fast that pivot grabs and pivot f-tilts can mess up Villager's attempts to get some space and set up shop. Also surprise Hammer Spin Dashes can nab him out of the air or on the ground.
I do play other characters, but these are the 4 I've been using the most, recently.