Sorry for taking a few days to reply - I'm glad to hear you're enjoying playing!

You're right about the convenience features, it's something that I'm working on bit by bit with each update.
Polish wise, again this is something that is going to come with time. Some elements are pretty much as I'd like them sans some beautification or tweaks to make them more obvious, others however I'm not happy with and are going to be redesigned in a future update. A good example of this is the supplyship and trading system. As a feature I like them and they work well, however I am planning on totally redesigning how they occur, what they offer and even how they look (I'm planning on using the top right of the screen for a minimap so I need the space

). There is going to be a minor update to some of these points in build 4 which will be released next week, but the major reworking will probably come in the 8.2 build. I've deliberately left a number of elements slightly 'raw' because I have so many things to add to them in the coming months.
For a first alpha, 'isometric, single player, squad based survival minecraft' is actually pretty much what I was going for. At this stage all the core elements of the game namely AI, events, world exploration, mining and building, unit 'awareness' and mechanics and combat are present and it allows people to get a good feel for the game at it's most minimal if that makes sense. Now that the foundations are there, the really exciting work starts for me as I take each element and add new parts to it - new weapons and ability to change loadout for units, day and night cycle and lighting improvements (all coming in the first major update 8.1), new enemies and neutral creatures to harvest for biomass, dynamically created quest system (I notice you mentioned this in your post) based on organic events in the world to mention only a few. It also enables me to get feedback and suggestions from players some of which have already made it into the game.
When there's an event notification in the game, you can hit [ENTER] and you'll be taken to the source of the event (some events don't have a location though i.e. a resource trade notification). In build 4 there are also big improvements to combat and under-fire notifications as well! Group selection is on my task list but I'm not sure if it will make it into 8.1, if not then 8.2, I agree this will help a lot when it comes to small squad orders. A funny anecdote is that human entities actually are dynamically named in the game (originally in the first few proof of concept builds you played as the humans), adding the ability to name (and rename) your troops is something I'm looking to add soon as it helps with the RPG aspect if each unit has a proper 'identity'.
Continuity wise, what I was thinking was having a number of dropships ships progressively getting bigger and with more starting troops + facilities which are unlocked through play. So, for an example, to unlock the second drop ship perhaps you would have to destroy five enemy bases in one world .. again I'm not 100% on how it will work but that's the idea currently.
On the subject of LPs and monetisation, I have no problem at all with either (there's a
section on the FAQ page of the Isomer site covering monetisation, short version go for it

- I actually get a real kick from seeing what people do in Isomer, there are a couple of fun
show and tell threads on the forum. It's a good suggestion, I'll try approaching a few LPers and see how things go - thanks