But is it affordable?

The one and only Wii U eshop game that comes into my mind is Affordable Space Adventures. It uses the Wii U gamepad very well and you can also play it together with another person in the same room. It's a ton of fun. Besides Fast Racing Neo the best third party title on Wii U. It was shown on Nintendo Treehouse Live during E3 2014.

I've been wondering the same thing myself, and was a little surprised no one had made a thread yet. Was planning to do it myself if no one else did.

From personal experience, Affordable Space Adventures is great. A must own for Wii U owners. I just downloaded Pushmo, and that is a pretty cool puzzle game. I want to check out the other games in the Pushmo series. Pokémon Picross is a great puzzle game if you like Picross puzzles. BoxBoy is a pretty cool puzzle game, and it has a couple of sequels as well that I want to check out. I really liked Fluidity on the Wii, and there is a sequel I am going to download on the 3DS called Fluidity: Spin Cycle

I found some articles out there:

• https://www.gamespot.com/articles/the-3ds-and-wii-u-games-you-should-buy-before-their-eshops-shut-down/1100-6500804/
• https://www.nintendolife.com/features/29-best-3ds-eshop-games-you-should-get-before-theyre-gone-forever
• https://www.nintendolife.com/features/23-best-wii-u-eshop-games-you-should-get-before-theyre-gone-forever
• https://ftw.usatoday.com/lists/best-3ds-games-eshop
• https://ftw.usatoday.com/lists/10-wii-u-games-eshop-shut-down
• https://sea.ign.com/xenoblade-chronicles-x/182108/news/games-to-get-before-the-nintendo-3ds-and-wii-u-eshops-shut-down-forever

Highlights seem to be:
Super Mario Advance 4: Super Mario 3 (Wii U) for the bonus e-Reader levels.
Xenoblade Chronicles X (Wii U) because who knows if the data packs that improve performance will be available.
Any of the Virtual Console games. Personally, I am looking at stuff like Earthbound and Earthbound Beginnings, Zelda - Oracle of Ages/Seasons - Minish Cap - Phantom Hourglass - Spirit Tracks, Advance Wars Dual Strike, Pikmin 1 and 2, Pandora's Tower, Metroid Fusion and Zero Mission, Golden Sun 1 and 2.
Hard to find/expensive physical games. I've been looking at stuff like Kid Icarus Uprising and Bravely Default on eBay the past couple of days. Physical copies seem to be going for the same or more than digital. I'm worried once the digital versions go away, the physical versions price will go up even more.

Unfortunately, I am probably looking at spending $200+ across both shops before they shutdown.

If anyone finds other articles, please post them.

Metroid Prime Trilogy. It's one of the reason I still keep my Wii U (another is Super Mario Galaxy 2). 

Edit: I checked and it's a Wii release so it might already be inaccessible depending on if the Wii eShop is still open.

I checked more carefully this time and it has been re-released on the Wii U eShop.

Yeah, it's a sequel to one of the ending routes of IV. 

Earthbound and Earthbound Origins would have for sure topped this list but I guess with it now being released on Switch it is a bit of a moot point. Other games worth looking at in my opinion are Golden Sun and Golden Sun II: the Lost Age, these are both very fun and solid RPG's that are quite underrated.

Anyone has something to say about Kirby and the Rainbow Curse ?
It looks to be a unique game and the reviews and opinions looks to be mixed about it.

Tagging for later, but can confirm that Affordable Space Adventures was a ton of fun.

I got it on the Nindies Humble bundle too. I didn’t play any of the games in the bundle but just couldn’t pass on the deal. I had no clue affordable space adventures was such a highly recommended game. 

I have it and I quite liked it, but it's not for everyone. It took me a while to get accustomed to the stylus controls.

On topic: Fire Emblem Fates Revelations. I think this is download-only.