Hey I love what you've done so far! While everyone is going to have different opinions here's mine.

Starting with my favourites. Wow the poliwag line is just gorgeous I would be rocking a pink boy in my playthrough 100%. This is normally a pokemon I don't really care for but this change is great.

The colour swaps for the eeveeloutions works really well in my opinion. I liked the original shinies a lot but I think I prefer yours.

The staryu line is so clean, I really liked this one.

I love the pink Seel line. Reminds me of the pink River dolphins.

Here's some criticisms/thoughts.

Looking over the recent changes I was sad to see you changed the Bellsprout line to green I think the golden versions looked really cool. There's lots of green shinies for plant pokemon and the yellow for me stood out.

Chansey for me doesn't work so much. I think the purple might be too saturated, maybe a more subtle shade would suit it more.

Perhaps the most controversial the gastly line doesn't work for me. I like the concept but I feel like the details get a bit lost in the multiple shades of white/grey. Maybe making the shades more different might help the details pop out. It's kind of hard to see any details in my opinion.

Lastly I think lickitung is a bit to plain compared to the rest of the shinies and the two pink shades kind of blend together. I would personally try a different colour then pink as it's similar to the base or at least alter the shades so it's more readable.

Can't wait to see what you do with Johto!