I think combining the Kree/Skrull War with Secret Invasion is a great idea.
And I love that they started planting the seeds for this with the online episodes before the season even started, then kept adding stuff both with Madame Hydra, the Captain Marvel episode, the Kang stuff, and the final episode.
Kind of like how they set up Doom with the very first scene of the premiere.
They've done some really good stuff setting things up for future episodes, while still mostly having self contained stories most weeks (with the notable exceptions of the two-part premiere, the Loki stuff to end the year, Ultron, and Kang). It's a really well done show.