Yeah, all that super soldier shyt was added at the last minute. Basically anything past the episode you're talking about, with the Syndicate being burned, they had to make up as they went along.
Season 6 would've been the last season. That's why, like you said the season finale "Biogenesis", and then the first two episodes of 7 "The 6th Extinction" and "Amor Fati" were a totally different angle for the myth stuff.
Although honestly all 3 of those episodes were dope as fukk. The problem is they couldn't freestyle for 3 seasons. If 7 was the last they might've been able to keep it up and close it out strong.
As far as the finale, I thought it was awful. But it is what it is, like you said it's virtually impossible to end something after 200+ episodes and 9 seasons. By season 9 I was just watching it out of loyalty more than anything.
Side note, "X-Files" being stretched out and ending poorly is why Vince Gilligan ended "Breaking Bad" after 5 seasons. He was a writer on "X-Files" for 7 seasons and didn't want "BB" to go out like that.
Fred.