Eliminate the install silos
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One of the cool things Apple did with Mac OS X 10.5 Server is to make setting it up simpler for those with simple needs, i.e. the "Workgroup" setup. The problem is, the setup types are fairly siloed. For example, if you use the Workgroup setup because you want some really cool features, like importing Active Directory users for augment records, or ease of setting up iCal Server, you're unable to get to any features outside of what you get in Server Preferences. If you attach to the server in Server Admin, and you say you want to now use it in "Advanced" mode, you can't use Server Preferences with it. No big deal, right? Well, it is if you want to create more augmented users, because in "Advanced" mode, you have to use Workgroup Manager for user management, and Workgroup Manager can't import Active Directory users to create augment records.
If you install simple, you can go advanced, but you can't go back. If you install advanced, you can't use any of the simple features. In my world "Advanced" doesn't mean "more crippled than simple." Sure, you can create augment records manually, but why? This is silly. Even worse, to even see augmented users, you have to enable "Show All Records" in the preferences, and then manually find the "augments" entry, to even see them. "Advanced" is not synonymous with "make it harder than it needs to be."
Eliminate "almost" setting up services
As a few people know, I'm a big fan of SNMP, and in Mac OS X 10.5, and Mac OS X 10.5 Server, SNMP got a huge update. But still, to set it up on server, the only thing you can do with Server Admin is to turn it on. To configure it, you're deep into snmpconf and the .conf files. Really, it's not hard to put a decent UI on this. If Apple was smart, they could lead the way towards encouraging the use of SNMPv3, which allows for encryption and "real" authentication. NTP setup? On/off. No way to set any options. Same thing with SSH.
Make Directory a bit less restrictive
The Directory application: Great way to set up groups, resources, etc., in Mac OS X 10.5 Server. However, if you have more than 500 people/groups/etc. in your directory service, well, good luck browsing that list. Directory will not display all records if there are more than 500 entries in what you're displaying. You can't even manually select it.