So I am looking to play a 50/50 class from the beginning in an attempt to solve this.
- Leveling every other level in each class reduces "meta" leveling and acts more like
a new class instead of picking and choosing levels in each to "control" skills.
- The story background is a combine origin, a special sect.
So you don't damage story picking up levels in the "cross class" its just part of your progression.
The problem is that you can't just 50/50 any two classes because you can gimp yourself.
The result will be a resounding "If I have told you once..." speech from my GM.
Multi-class rules are designed for dipping. They make very crappy 50/50 characters, and I actually suggest avoiding it at all costs. Especially with spellcasters. Trailing behind one or two caster levels is doable, but several? The lack of high level spells known HURTS; the spell slots aren't enough. I speak from experience. Hybridizing casters is not very good; you're better off asking the GM for a custom subclass that gives you access to specific spells you want for your concept rather than attempting a hybrid multiclass.
I don't really spend enough time with dedicated martial characters to know if multi-classing them in a 50/50 manner will work, but my knee jerk reaction is to wonder if putting off that Extra Attack until level 9 is going to be worthwhile. Rogue looks good, since there is a linear growth instead of the bumps at the tier milestones, so they're good to mix with other things to make up for the loss. I don't recommend two melee classes that rely on extra attack, and since rogue is the only martial class that doesn't have extra attack....
Would you as a GM have any problem with these multi-classes?
Why?
Well, there might be a complaint that you're just effectively making a Nature Cleric or Shadow Monk using alternative features. *Shrugs* I'd probably suggest including bits about ties to both a monastary and theif guild for your ninja character. And the druid-cleric might want a nature-based temple.
Good luck with everything.
Others have mentioned warlock often, and that's because the main source of power for warlock is the cantrip Eldritch Blast. That's pretty much decoupled from the class level progression, so warlock mixes well with other things usually. Take your pick of what else you want for flavor.
If your DM is a "story teller" type, why does he even care about levels etc? Those are not part of the story, unless he has organizations or such in the game world that award class ranks to members?
Yes, levels are part of the story. All mechanics have story reflections. People often decouple story from mechanics, but that doesn't mean the story doesn't exist in the first place.
Don't insult other people's playstyles just because you don't like it.