If you want to use a squishy warframe, just throw on a bunch of survivability mods. Health, Shields, Armor, Flow+Quick Thinking, etc. You shouldn't be taking much damage at all tbh, unless you your team is ignoring adds, and you are standing directly in front of attacks or something.
Unfortunately I don't think it's very reasonable to expect that DE is going to balance 140 warframe abilities for each of these boss encounters. In a game like destiny where there is only a handful of abilities to balance it's way more doable. But DE could balance it around 1 ability that works against a boss for every warframe bringing down the total abilities to balance to 40, that's a start I guess. I hate restricted metas, they sap the fun and creativity out of any game. I agree with you something definitely needs to change.