Cut off one head and two shall grow in its place.
Protean Hydra may not seem like anything special, but it has lots of character and really captures the mythology of the hydra. Its just a fun card, even if its not the best. Yes, it dies to spot removal, but so does almost anything else. I will agree that Protean Hydra by itself is fairly underwhelming, however, when combined with the proper pieces, it can spiral out of control very quickly.
Counting for Fungus
The real star of this deck, Corpsejack Menace boosts the effectiveness of almost every other interaction. The last ability of Protean Hydra for example, already doubles the number of counters removed from the creature, but just a single Corpsejack Menace on the field will quadruple every counter removed! If you were to cast a Protean Hydra for 3 mana (coming in as a 2/2) with a Corpsejack Menace already down, then removed a single counter from him... he would already be a 5/5 at the beginning of the next end step!
Playing with Your Ooze
Ooze Flux is the core machinery to growing a massive hydra, or an army of oozes. The drawback of the abilities of Protean Hydra is that (by default) you have to attack or block to grow the number of counters on him. Since the ability triggers for ANY reason counters are removed, we need a way to manually activate it. Enter the Ooze Flux. For a measly 2 mana, we can strip any number of counters off of the hydra to trigger the doubling AND create a token as a result. As an additional bonus, if Gyre Sage or Renegade Krasis is on the field, you can also strip the counters off them to create an even bigger ooze and re-trigger their evolve ability when it enters the battlefield.
Other Interactions
What happens if you don't draw a Protean Hydra or Ooze Flux remains buried in your deck somewhere? Fear not, the deck is built in such a way as to allow interaction between all of the elements without relying too much on any single one.
Bioshift is a wonderful instant which allows you to manually grow a Protean Hydra, double some number of counters just by moving them around with a Corpsejack Menace on the battlefield, or if a creature can't be saved from spot removal, you can at least save its counters by moving them somewhere else! It can also be used offensively, to shift counters onto an attacking creature that would otherwise die to a blocker, or shift power to a smaller unblocked creature to get more damage through.
Hunt the Weak not only adds a counter to a creature, but gives you faux spot removal if you have a creature with greater power than one of your opponents. This works great with Protean Hydra since you can target a weaker creature whose damage will ultimately make it stronger. Be very careful, however, against decks running any sort of instant creature buffs which could put the opposing creature into kill range for the hydra. Similarly, reducing the number of counters on the hydra to too low of a threshold will put it in range of burn spells.
The evolve mechanic of Gyre Sage and Renegade Krasis can be quite powerful, especially when combined with Corpsejack Menace doubling everything. An Ooze Flux can create as many tokens as you have mana for by pulling off enough counters to trigger both evolve abilities each time another token enters the battlefield.
Ring of Kalonia can give a massive hydra the trample it needs to swing through for a win, or simply boost a hydra or Gyre Sage for more power or mana. If a ring doesn't show up, or you need higher numbers of tokens to get around blockers, then Korozda Guildmage can be used to break a large creature (ideally an ooze token) into a lot of smaller tokens or grant intimidate for some much-needed evasion.
Improvements
Some playtesting will be required, but one of the things I may need to put in is something like Trollhide to provide better protection for creatures that need to stay on the battlefield. The defense boost would also allow Protean Hydra to attack, defend, or grow with near impunity since even with all counters removed the defense will keep it alive.
Against opponents running heavy removal, something like Canopy Cover or Alpha Authority is probably needed to help protect critical pieces of the puzzle.
Additional Considerations
Heroes' Bane certainly fits the theme of the deck, but I'm still on the fence. Admittedly, it requires far less moving pieces than Protean Hydra, allowing it to grow using only its own ability. The higher static mana cost combined with the inability to affect the number of counters it enters the battlefield with is a bit of a deterrent. Especially since its growth ability is twice as mana intensive as Ooze Flux without providing the added benefit of a token which can activate evolve abilities.
Spider Umbra can not only help deal with flying creatures, but it can also provide defense for a Protean Hydra to attack into much larger creatures without fear of dying, and provide additional defense against removal via the totem armor.
BUDGET NOTES: while Kalonian Hydra and Primordial Hydra would probably be just bonkers and fairly hilarious, they far exceed the budget for this deck... however, if you have the budget, or already have the cards, there's no reason not to test them out!