The dual-casting system is easy to work with as is, because they have it set to not dual-cast different spells (which is also why there aren't 20 different levels of fireball, etc. this time around). The problem is that created spells might have the same exact effect combined with totally different effects, which could lead to severe problems. Or trying to dual-cast a created spell that pulls from multiple magic schools if you've perked dual-casting in some, but not all, of the schools being used.
Both of those are again, easy fixes. The first thing you present isn't a matter of spell effects, it's a matter of Spell IDs. They have to have the same Spell ID to be dual cast afaik. I haven't really played a mage (mainly due to the severe lack of spells in general, combined with no spellmaking) so I can't say that for sure. But that makes sense to me that they would do it by ID rather than effect.
As for the other thing you mention, it could easily just add up the cost of each effect separately, checking them against the perks you have, and then applying it for a total cost and output, or it can just do a simple "If you don't have Dual Cast for a school and the spell has ANY effect from that school, no Dual Cast for that spell." Either way would work fine, and I would actually rather it be done the second way than the first way, as it would force you to perk accordingly for it.
And I just want to say now that I'm in no way just arguing to spite you, having a healthy discussion about game design is a passion of mine, especially when it is a series and a game aspect I am so passionate about. I was never the "OMG SPELLMAKING IS TEH HAXORS GOD MODE!!" player, I was just the person wondering why I, as a person with a huge magicka pool and a mastery of every spell school, had to carry a staff with a measly 13 charges to cast a spell that did a high amount of damage in Oblivion. Then I found how awesome spellmaking could be.