Edit: I thought the post I quoted here was by JRoush. Adjust pronouns accordingly.
I don't see how it would cause incompatibilities. All that would happen is that you'd gain SkillGain * DiminishingReturn^(N-1) skill experience for casting the same spell for the Nth time in a row.
Which is a problem if, for instance, a script has set a specific gain amount because it plans to
reverse that amount and apply modified amount as soon as it detects a skill gain. This is how range-based experience tends to be done, and that's just the first example that popped into my head without giving it any real thought. If the amount that will be gained by casting a spell is not the amount reported by GetSkillUseIncrement, you're asking for trouble.
But changing the actual increment on the fly is a bad idea too, partly because I know of several scripts which will overwrite that change, but also because there's no indication available to other scripts that your change is a temporary one: they might read it in thinking it's the base value, and save it for the entire game session. For that matter, an ill-timed reload would probably throw off OBME's assumption about the base increase rate. (Avoiding these problem was the original inspiration for my Progress mod, which is actually a shared platform for advancement-changing mods to know which adjustments are temporary and which are permanent.)
There are multiple "magicka-based skill progression" solutions. They use completely different formulas, so you're not going to be making them obsolete (in which case I'd have no argument), just competing. And I foresee a huge overlap in interest between the users of those mods, and the users of mods dependent on OBME... not least because I'll be the author of some of each.
Currently the big ones are Progress and Supreme Magicka, both of which make it easy to disable the feature (before even starting the game) for mutual compatibility. But OBME features aren't bounded by any single (or well-defined multiple) .esp or .ini file; I foresee troubleshooting headaches. Sure, it's off by default, but the problem is that any mod might activate it without properly documenting it.
That's my two cents. It's a great feature, and a popular one, and it does share a thematic space with much of what OBME does, but I think it's best kept separate for technical reasons.