Is it a problem that G and U both have a theme of "turning opponent's stuff into other stuff with counters"? Will people be puzzled they're similar but different?

I'm not sure if it is, and even if it is, it's probably best to just live with it, as both themes are good.

But if people think it's a problem, are there any other suggestions? I don't think expanding either theme into another color is likely to work well at the moment. One possibility would be to give green a very minor "turn lands into forests" theme and blue a very minor "turn creatures into fish" theme, so they mirror each other?

I don't think that we should make them more similar. If anything, we should work to differentiate them.

Keep them separate. If green only affects creatures, blue only affects lands, and both have very different flavor, people won't get confused.

As far as I'm concerned, my vote doesn't count. So, so far, we have one yay and one nay for the direction of Mono-Green. That means we need to find a compromise.

I agree with Link that moving the two mechanics together doesn't really solve the problem. In the end, we'll have a bunch of people wondering why blue and green look so similar and we won't have any good excuses for them.

Jack mentioned that we can put more of the +1/+1 counters on your creatures. I think we can go further than that. I do like the creatures that must put a +1/+1 counter on their opponent's creatures, but this could be dialed back a bunch. Meanwhile, green could be spreading a lot more +1/+1 counters, mostly on it's own creatures. Half (or more) of the creatures in green could start off not as fungus, so you have more creatures to turn into fungus. We could also make a bunch of fungus token producers... which would have no analogue in blue, and we could increase the amount of creatures that put creatures on the battle field. Llanowar Sentinel type of cards that could either be fungus or fungus bait.

The net effect would be that green doesn't care where the fungus came from... it just wants a lot of them. The more fungus on the table, the better. As a sub-theme, Green will sometimes not care if the creatures on the table happen to be fungus - a large pile of creatures and +1/+1 counters win the game on their own.

On the other hand, we can push blue in the other direction. Blue doesn't want the board to be filled with islands. Blue just wants its opponent to have one island. That's enough of a beachhead for blue to start manipulating the opponent. It means that we lose Serpent of the Endless Sea, but that's about it. Not a big problem, really.

Does this sound like a workable solution?

Edit: Even though Dude's comment came in 30 minutes before mine, this post was posted before I saw it. I don't think that changes the content of this post, though.

I definitely like the idea of focusing green a bit more on "loads of fungus everywhere, don't care whose they are", and I also think it's a very good idea to have a couple of green token makers and/or a Llanowar Sentinel-style card.

In ~Green Plane~ I've been working on separating Green into two facts: Fungus and Plants. Mechanically, the Plants could provide fodder for the Fungi to take over. I think Llanowar Sentinel types would make a good fit for plants.
As for the plants and their own mechanical theme: have there ever been cards that "care" about mana production? I mean, there's Omnath, Locus of Mana, but that's not quite what I mean. This might screw things up, but what a large portion of the plants had mana production capabilities, or searched for land when entering the battlefield? As worshipers of the sun, I see the plants valuing growth and energy. Perhaps there could be a creature that had "Creatures you control with mana abilities get +1/+1," or "Whenever a creature you control taps for mana, add to your mana pool (or do something else)," or maybe there could be a reprint of Dryad Arbor or a similar creature.
Anyway, making this a theme in blue will definitely differentiate it from green.

"Care about mana" sounds like an interesting theme. I'm not sure there's specifically a problem with where the set was going, but I agree it'd be a good thing to suggest some more simple green creatures and some plant theme green cards and see if the mix of stuff makes a good skeleton.

Intriguing idea. Reminds me of Glissa Sunseeker, or things like Sakura-Tribe Springcaller. Having a mix between finding Forests and finding any basic land would let the colour naturally support multicolour in way natural to the flavour.

I would rather have a "cares about mana" theme than a "cares about fungus" theme that leads to unhappiness.

I like where we're going with the plants idea. I'd say we work on the "plants make mana and overproduce" and "fungus tries to take over plants" at the same time. When we get to testing, we'll find out which mechanic is more fun, and/or, decided that the two mechanics work well with each other.