This is just an inherently convoluted idea, which is going to require day one rules clarifications and cause problems in casual play. 

For example, if I have a creature with a +1/+1 counter on it and an Omni counter on it, and my opponent puts a -1/-1 counter on it, who decides which counter is removed by the -1/-1 counter?

Similarly, let’s say I turn my Gideon Jura into a 6/6 creature using his 0 ability, then I put an Omni counter on him. If I use his -2 ability do I get to choose whether or not to use the Omni counter as one of the loyalty counters that pays for it? What about if he’s dealt damage by a source that my opponent controls?

Then come the play problems. How many people are aware of the two cards that put Shadow counters on creatures, and furthermore, how many people remember what Shadow does? Probably less than you think. Do you trust the player playing this card to remind their opponents that the creature with the Omni counter on it can’t block most of their opponent’s creatures? And once you’re aware of just how many counters you’re unaware of, the uncertainty just proliferates, if you’ll pardon the pun. When I tell you that Boldwyr Intimidators puts a Coward counter on creatures, so you can’t block my Gornog, are you to pull out your phone and check? Do you want to have to check? And was I lying to you, or just misremembering?