Sure, but those aren't the only two options. You can just pass normal laws. They don't have to be amendments. That's also difficult, though, due to the extreme partisanship in our political environment, but it's theoretically the fitting solution.
My understanding was that at least some of those - Obamacare and the EPA - required either an Executive Order or a Constitutional amendment, because the powers required were not granted to the Federal Government by the Constitution.
Agreed that declarations of war can just be declarations of war, no amendments required. It strikes me as odd that Congresscritters would be okay invading a country, but not okay with declaring war against them.
US Agencies don't need a Constitutional Amendment to come into existence - the usual method is simply a law that Congress passes that the President then signs. E.g. Dept of Energy, Dept of Education, Dept of Homeland Security, Dept of Housing and Urban Development, etc. going way back to the Dept of Foreign Affairs (precursor to Dept of State).
Obamacare (Patient Protection and Affordable Care Act) was also created by Congress - bill passed in both houses, signed by the President, upheld by the Supreme Court. That's basically a textbook example of how the system is supposed to work.
I'm not sure why the EPA (and others, like FEMA) were created by Executive Order instead.
As far as why Congress hasn't declared war since WW2, they've basically rolled up their say into the War Powers Act and the War Powers Resolution which provides for them being informed and issuing continuing approvals. They can then support the President (as Commander in Chief) but not officially declare war.
My understanding was that the IRS was directed to enact Obamacare by Executive Order, because they (the Federal Government) have no Constitutional mandate in that area. Same with the EPA.
