These problems become less pressing with a less sequentialist understanding of action order in D&D 5e, which admittedly doesn't make them any more intuitive or realistic. But if you model that Action and Bonus action aren't necessarily meant to be happening sequentially the idea that you need both hands to attack with a two handed weapon and that means you don't have a free hand for your bonus action that requires it makes more sense.
It's not like, each of your action, bonus action, and movement take two seconds that you get to order how you want, it's that doing these three things approximately simultaneously takes six seconds, your action is the main thing you are focusing on accomplishing for those six seconds, and your bonus action is something you can do basically at the same time, and you can do both of those things while moving.
So if your main focus is attacking with a two handed weapon, you don't necessarily have the time or attention to take your hand off the weapon and do something else with it even if you could do that with only one hand occupied. One use of the Attack action doesn't strictly correspond with one swing of the weapon, it is spending six seconds trying to attack someone.
Admittedly, the turn-order structure of combat kind of clashes with this, and the fiction narrated by every character taking their full turn in order doesn't really line up with this understanding, especially with "non-action actions" like talking happening on or between turns.
A thing I find helpful is to remember that bonus actions are not promised, they are earned and if you don't fulfill the requirements for taking a bonus action you can't take it, because it's a bonus not a promise.
Only monks can make bonus action unarmed strikes because they're the only ones sufficiently skilled with their fists for that to make sense, anyone else is just spending their turn punching, while anyone with a light weapon can get an off hand jab in.
"off hand unarmed strikes" from people wielding weapons are better modeled by things like Battle Master Maneuvers than by using the off hand weapon rules to model punching someone while swordfighting.
Extremely unhelpfully, I like to run combat in 5/5.5 without turn order, taking every player's "order" of what they want to do with their turn and resolving it all simultaneously, and resolving conflicts that emerge over action order with one-off initiative tests between the characters affected (did I get out of range before his shot went off? Whose attack connected first? Can I run away before he reaches and hits me? Things of this nature). This makes it feel less like Move-Action-Bonus action are happening in sequence where it doesn't make sense that I can't do something with my off hand now that I've "finished" attacking with my greataxe.
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