I have expressed my preference for the thermal clip system in the past and in this thread.
Now I am not against a return of the overheat system, but the crux of the argument for the overheat system seems to be "I do not like running out of ammo!" which I think is kind of dumb.
My distaste for the thermal clip system has other bases:
-- I don't enjoy running around after every battle to pick up thermal clips. It breaks the urgency of the mission's pacing and is generally unfun.
-- Thermal clips seem out of place in some areas. It makes some of the levels feel more like... video game shooting galleries rather than natural environments.
-- Lorewise, it's a step backward.
-- Skillwise, it favors player aim over firing rate management.
-- Running out of clips or relying on clip availability at the mission site means my character does not properly prepare for the mission at hand. Role-playing actually matters to some people who are playing role-playing games.
-- Weapon cooldown goes hand in hand with power cooldowns - which also became ridiculously fast by ME3.
-- It also restricts some playstyles.
I'll try to explain that last bit: I sometimes play characters who won't rezz fallen squadmates. If squadmates fall in battle, I need to finish the battle alone. I get through most missions using only my primary weapon, but when squadmates fall, I often need to switch to a secondary and sometimes tertiary weapon. With ME3's weight system, I carry these weapons only as backups, and pay a price in power cooldowns - and it is entirely because of the thermal clip system (and my preference for not rezzing fallen squadmates).
I have fond memories of my first play of the Citadel DLC. Once my soldier found that Lancer, she carried nothing else for the rest of the game, and was delighted to once again have the challenge of managing weapon overheating without having to constantly chase thermal clips.
It is certainly unique and I enjoy playing with the overheat system in ME1 from time to time. But ultimately I think it leads to less weapon variety.
How so?
Properly designed, I see no difference in the potential weapon variety.
Now the weapon overheat mechanic can work decently well with low damage, high rate-of-fire weapons like most assault rifles, pistols, and SMGs. These weapons tend to have large clip sizes, so an overheat mechanic could translate well if implemented. However, it becomes somewhat of an issue with other weapons, particularly weapons built around high burst damage. It would still work with some or most shotguns and sniper rifles, but it becomes a big issue with the outlier weapons.
During my infiltrator run, I really wanted to use the Incisor as my primary weapon - but it's 3-shot bursts combined with low clip limits made that not work very well in some situations. With a cooldown rather than clip system, I could have enjoyed using it.
Your discussion of specific weapons are all things that can be dealt with in weapon design. Giving each weapon a unique value of heat generation per shot and cooldown per second can provide just as much weapon variety as set thermal clip limits.
My suggestion RE chargeable weapons is that they generate heat (causing heat buildup) while charging and retain that heat until fired, at which point the cooldown can commence.
This is why I want a thermal clip system. If you want to have some overheating weapons like ME3 did with the Prothean Particle Rifle, Collector SMG, and Lancer, I can live with that. (I would dislike it, but I can live with it if they feel balanced in some way like very low damage.
Very low damage? Why?
And proposing a hybrid system, whereby weapons overheat but you can bypass the cooldown with thermal clips, is a dumb proposal. What you are essentially saying is "I do not want to ever run out of ammo or reload my weapon!" because... you suck at games? No seriously, why do you want that system?
Or they could be, yanno, trying to find a compromise for players with mutually exclusive preferences.
Believe it or not, some people actually enjoy the challenge of dealing with weapons that can overheat, without the get-out-of-jail-free-now card that thermal clips provide.
In ME1, enemies could overheat your weapons, forcing you to change weapons or wait for cooldown. The thermal clip system made that mechanic irrelevant.
The overheat system is supposed to punish you for firing too much at once, while the thermal clip system is supposed to punish you for missing with a lot of shots or overly-relying on one weapon too much. You basically want all the perks of both systems but without the drawbacks of either system.
The thermal clip system punishes the soldier class for relying on firearms and having no other enemy damaging powers. Combined with ME3's weight system, it punishes anyone who carries extra weapons for backup in case you run out of clips.
Of course, some people play games for pleasure rather than punishment.