I wasn't considering the Shield before because I need Amazon Prime and Plex. I don't really like the remotes that come with the Shield and would like to use a boring universal learning remote.
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Get the new Shield and use a Flirc.
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Buy a used first gen Shield (and program my remote how?).
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Buy a new Shield and suck it up and use the included remote.
If you get a Harmony with a hub you can just use BT. I use FLIRCs in all my media PCs and love them, so you can't go wrong with this approach either. Harmony IR blastings works flawlessly, not sure how to deal with other brand remotes though.
Amazon has refubed Gen 1s up from time to time, shipping is pretty far out though.