I don't believe the mod manager should be included in the default distribution. Modding may be the only way to expand phpBB's functionality, but it's by far not for everyone. Including an automated mod manager into the core product is too much like an official "thumbs-up, anyone can and should use this" and I don't think that's a good idea at all [at least not at present time]. Modding will always be for the more experienced users, because especially the way it works in phpBB, there are problems lurking that no automated mod manager can overcome. Offering it as a separate download is a great way to emphasize that. I also think that anyone that wants to download an automated mod manager should be able to prove they have installed at least five mods the manual way

(Of course, only kidding, but I do think that, when installing MODs, people should be aware what is going on. People nowadays are used to squeaky clean plug-in systems from e.g. modern browsers and installing a phpBB Modification may look a lot like that when using an automated tool, but what's going on under the hood is a completely different ballgame).
One thing I would very much like to see in 3.2 is phpBB using as much as possible its own extension mechanisms. Currently, there's a separation between standard and custom profile fields and bbcodes. Ideally, the "standard" parts would just be default configuration, not using completely separate code. When I read reports about a new bbcode interpreter, it seems that's exactly what's being worked towards
I agree to an extent that relying on code changes for modding is not ideal, and I think it is a good idea to work towards cleaner mod installation. We should not forget, however, that the current system is extremely flexible, and that it does have its advantages over a more modular, hooks-based system, as well. I think that the direction taken with the module system for the various control panels is a great one, and hopefully the team can expand on that and make more parts of the system modular like that. Hooks at strategic, non-performance-essential places sounds like a great compromise. Maybe at one point, when a good number of mods MODs can do completely without editing core files, that integrated mod-installer would be a good idea after all
