i’m the author of SCT (sphene community tools) - just wanted to give my point of view on the flaws you mentioned (i fully understand that it might not be the perfect solution for you):

1. different apps - I wanted to create a forum and a wiki .. and build it together for my website.. What was clear pretty early is that there is quite a bit of functionality which needs/can/should be shared between those two applications. So i decided to put them together into one bundle.. where there is one ‘community’ app with all generic methods (middlewares, registration, etc.) and two separate apps wiki/forum (although the separation isn’t perfect yet either)
- would it be easier if i would have created 3 separate projects for this instead of putting it into one repository?

2. you only need two middlewares and the application template loader.. - i don’t know how to do it differently .. except merging it into one middleware.. which wound’t be much improvement

3. there are a handful of unfinished functions.. but there is a reason for why it uses that many lines - the structure isn’t perfect yet.. and there are a few hacks.. but in general the idea is that you have a generic forum app . and can plug in whatever you need without modifying the core application. so in my opinion.. these few extra lines make it easier to extend.. (there is a linklist category type, blog category type, Q&A category type, etc. all extended the functionality of the forum without modifying the code to remain easily updateable ..)
of course.. if you just want to hack in your changes without caring about if you want to ever update to the latest version it would be easier to specifically implement those features in the core.. instead of going that extra mile to provide extension points..
but i like flexibility .. which is not right for every project i guess

so i guess you got the evaluation right, just wanted to point out that most of these flaws have reasons

cu,
herbert