I have a lot of trouble to finally make to full installation as this requires some experience. I would ad that the biggest problem using this OS is time (beside some broken links) needed for compiling every peace of software. After installing Mate it took a really long time to compile essential software such as Firefox.
So I would suggest some sort of repository and perhaps packages similar to deb,rpm, aur. Or perhaps some way to faster compiling.
Also there is no explanation or list of which programs can be compiled using alps install command.
Also what is the procedure for programs not in this scripts. For example I want to install WPS office package and I have DEB files but how to make it work here. What about open VPN, True crypt, GNUpg utilities and more.

Also is there anything similar to synaptic? How to install Conkymanager along with conky? How customize login and make a bit more beautiful (like elementary) . How to customize Plymouth?

I agree with most of the things that you are saying and we would surely take your inputs into consideration. Thanks for pointing them out. I believe apart from the problems in build process itself(which is time consuming and error prone owing to broken links), another problem is in the lack of documentation for a lot of things which come after the process of building is over. So we would surely add more docs for things like installation from debs, packages that do not have build scripts etc. As for a GUI based package manager is concerned, work is in progress on the same(basically an alps frontend). By the next release, the GUI package manager would be ready. I am also figuring out ways to make the build process robust and failsafe, definitely scripts need to deal with broken links automatically and or need to switch to other URLs for download without intervention. Would surely see how things can be done better in that regard as well.

Thank you very much for your feedback. Really appreciate it.