First of all, I have to say THANK YOU for making this happen. I think the world of international shogi desperately needed a server with all of these features that chess websites have had for years.
I am aware that lishogi is still in development and I would like to give some suggestions that I think are either necessary to implement or that it would be good to have. Of course, as this is a fork of lichess, being a developer myself, I can understand how there could be difficulties with implementing some of these features without messing up the code, but I will list them anyway.
1. Game thumbnails
By this, I mean the mini versions of ongoing games that you can see on the main page, like this 
As I'm sure you know very well, pieces in hand are a crucial part of any given shogi position. It would be good that they are also included with these minified boards so that the user doesn't have to click on the game and open it in order to see them.
2. Playing piece in hand by clicking
It is possible to click on a piece that's already on the board and then click on a square where you want to move it, but it isn't possible to do the same thing with pieces in hand. This poses a significant problem on mobile devices because it isn't easy to have to drag a piece all the way from one end of the screen to another, especially when in time trouble. I think it is important to be able to just tap on the piece in hand and then tap on the square you want to drop it to, as an option.
3. Arrows for pieces in hand or the equivalent
Currently, there is no way to draw arrows from pieces in hand. This of course would not look nice anyway, so I think there should be another way of indicating drops. It could look similar to how engine calculation is visualized, with "ghost" pieces indicating drops.
4. Byoyomi
As I'm sure you already know, byoyomi is an integral part of shogi. I do believe that no-byoyomi option should be there (it would be my preferred option most of the time), but I think it is essential that there is an option to use byoyomi. Honestly, I don't think that increment works really well, but even if it's kept, byoyomi still needs to be an option.
5. Better engine
I'm not sure if you're using some Stockfish version adjusted for shogi, but it really isn't very good. It makes pretty bad moves in the opening, but later in the game it tends to make more logical moves, some of the time. For example, this is a horrible move, and it is played by Level 8 engine, which is the highest level 
There are many open source shogi engines that are a lot stronger than this one.
6. Importing games
To the best of my knowledge, there currently isn't a way to import games (KIF format) into the analysis board. It would be awesome to have that feature because games from other servers such as 81dojo could be imported and analyzed in lishogi with its far superior analysis implementation.
7. Quick pairing
I'm sure you already planned this one, but the server needs to have a much larger number of players in order for it to work properly. It would be awesome to just click on the time control button like in lichess and get to a game in a matter of seconds. I hope lishogi will become popular soon.
8. Additional piece sets
I think the available options for different board looks are awesome, but I think that there could be some improvement in how pieces look. First, there's six versions of one internationalized set, which didn't receive too much praise when it was first introduced. I personally don't believe that using international sets should be encouraged in shogi as I believe it does more harm than good in the long run. It should still be an option, but I'd rather have more traditional piece options rather than so many "internationalized" ones. The 3D ones are a bit too small and I think having pieces that look similar to those on 81dojo would be great. Also, there are designs such as the one used in NHK cup that just look awesome in my opinion.
I can contribute by tracing this font and sending it in vector format if you'd be interested.
That's all for now. Again, thank you from the bottom of my heart for creating lishogi. I hope it will become THE shogi website to play on in the near future.
Several suggestions
One more I just remembered.
9. Handicap games
Since handicap games are such an important part of shogi, I think it should be good to have a way to quickly set up these.
And as was solving CAPTCHA in order to post this, I noticed that it's not working properly. It doesn't give an option to promote pieces, so you end up with a situation like this which is registered as mate, but it's not actually mate. 
Regarding item 8, I for one am very grateful for the international sets. Would love to see more.
I have to agree with patientZero about point 8.
I have the interest myself to try and learn the pieces but I can imagine many people will be put off trying to remember the difference between ~14 different pieces, and how they move. I don't think one should discourage or encourage any particular set really, to each their own, and hopefully the site just takes off and gets more regular players.
The other improvements sound good, although I've no idea myself about Stockfish since I'm a complete beginner :)
Luckily I could solve the CAPTCHA puzzle though...
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