As Philip would no doubt testify, it's always tricky to decide which packages to include/exclude. You could ask ten different people to make their application list, and no doubt you would get ten different lists back.
For example, I had previously been a big fan of wicd, but now I occasionally use a 3G modem, I find that NM0.7 is by far the best option for me.
The default cruncheee isn't perfect for me, but it's as close as I'm going to get without rolling my own. If, as his right, Philip takes out a favourite app of mine, then fine, I'll just apt-get it back! 
Having said that, everyone is entitled to express their opinion, and I'm sure Philip takes into account those opinions when deciding what to include/exclude, even if he isn't able to please everyone.
For the record, I like:
- PCManFM
- NM 0.7
- transmission-gtk
- ClawsMail
I don't like:
- LXDE (tried it with a previous distro)
- elmuratos scripts (not that I don't like them, I just prefer eee-control)
- deluge
Should there options to install alternatives during the installation?
I don't think so, because:
- The list of alternatives still won't please everyone
- If the list of alternatives is increased further in a bid to please everyone, you no longer have an install CD, but an install DVD, and I have a lot more blank CDs than I have blank DVDs...
- I like the fact that I can install crunchee in around 20 minutes from scratch, and only the first five minutes need be supervised. Having to go through tonnes of options at installation time will slow down the installation, and will make it more confusing for new users.