Welcome and thanks for taking minute to share those suggestions with us.
No. 1. attempts to solve valid problem, however I am sceptical if popup is right way to do it. Imho it would be better to display "There are threads like that: (list)" under thread name field in new thread form. However it wont be happening before 1.0 release.
No. 2. is just fancyness and I dislike stuff done for sake of looking fancy.
No. 3. needs some more elaboration.
Misago is not distributed with emojis smiles, it simply has out of the box support for them. If you want to enable emojis, you have to upload and enable them manually by uncommenting parser extension in config.
It won't be hard to include additional, configurable extension allowing you to use custom emoticons pack (like selected few emojis instead of all 800). This is now issue #213 on Misago and will come in 0.6 release.
On the sidenote, Emojis are nice beacause there are many of them, they are high resolution (so Misago can resize them to match text height) and everybody that has MarkDown has Emojis.