js gurus will decry jQuery - "learn to do it by hand"
php gurus will decry Wordpress - "it's a mess, learn to do it by hand"
and ... wow - front-end developers decrying bootstrap - "it's a mess, learn to do it by hand"
They're all not entirely wrong, but the specialist nature of their roles should not be ignored. Do you have a team of web devs ready to build something that is vital to your business and will be mission critical? Building on something that's not wordpress might be a good choice.
Are you trying to squeeze out every ounce of bandwidth performance and CPU optimization? Yeah, jQuery might not be the best choice.
But these libraries/products work "good enough" for so many people that it'll be a long time before anything dethrones them as the 'go to' tool for problem X. There's too much of an ecosystem built up around each one.
EDIT: I say this as someone who is generally pretty anti-wp, but I still recommend and use it for certain projects, it's just not my default go-to for everything.