I think there's several different questions to be answered surrounding server/game administration, since there's potentially many different groups of people involved either in the administration or the 'being administered'..
Generally you have this kind of hierarchy going on:
-
Server owner
- Responsible for making sure the server is up and running
- Wants the server to be clean and playable at all times
- Would like being able to monitor the server and do any vital work on it remotely
-
Administrator(s)
- Responsible for keeping a good atmosphere in-game
- Needs tools to be effective
- Would like the ability to not have to be in the game in order to do his/her duty
-
Moderator(s) + any other intermediate admin levels
- Usually responsible for minor incidences
- Needs access to limited tool-set, usually restricted to in-game usage
- Needs ability to report back to administrators on larger incidences
-
Players
- Want a clean, competitive atmosphere
- Want to be able to reach the appropriate people to deal with incidences
- Want clear feedback on what's happening and why, whether it's related to themselves, others or the server itself!
And here's my splurg of server config/administration commands/options etc I can think of:
-
Server administration
- IP / Port / Server name / Server tagline?
-
User groups
-
Administrator list - all account names (or IDs) listed are given administrator privileges
- /permissions add [name] "admin"
- /permissions remove [name] "admin"
-
Moderator list - all account names (or IDs) listed are given moderator privileges
- /permissions add [name] "moderator"
- /permissions remove [name] "moderator"
-
Both lists
- (you get the picture, use the name of the user level to add/remove permissions, this way you could have many host-defined user levels defined in config with a list of different commands that the user level can access)
- /permissions reset [name1] [name2] ...
-
Player Whitelist (+ option to enable/disable whitelisting) - make the server join-able only by those in the list. Allow moderators+ to add accounts to this list, or in general be able to change the list on-the-fly.
- /whitelist add [name1] [name2] ...
- /whitelist remove [name1] [name2] ...
- /whitelist removelast
- /whitelist reset
- /whitelist enable
- /whitelist disable
-
Player administration
-
Banning
(or in general, a 'banned accounts' list) - time-based bans, I guess recording the initial length, the admin who did the ban, the unix timestamps for the start and expiry date-time and a reason. Would be nice to have a list of expired bans recorded somewhere as well, to check if a player has been previously banned. So on player join, check if in banned list; if in list, check if expiry has occurred; if expired, remove from banned and add to previously banned list 
-
/permissions ban [name] [time_amt] [reason]
e.g. /permissions ban JP 3d (would ban for 3 days)
e.g. /permissions ban Grandy 5h (would ban for 5 hours)
e.g. /permissions ban Rockitz 0 (permanent ban)
- /permissions unban [name]
-
/permissions viewban [name]
e.g. /permissions viewban JP
JP was banned for 3d by Grandy for "being too sneaky" at 14:50 on 29/05/2015 - 2d 22h 48m remaining
-
/permissions viewbans
(displays the full list with similar format to the above)
-
/permissions history [name]
(look-up for previous or current bans for an account)
- Muting
-
/mute JP (mutes for the remainder of their current play session, also used as a local mute for players)
-
/permissions mute [name] [time_amt] [reason] (similar to bans)
-
Kicking users
-
/kick [name] (Temporary removal from the server)
-
Switching teams
-
/setteam [name] [number] (number could be 1, 2 or even 0 for moving someone to spectator?)
-
Observing users
This may be more something that could be added through a spectator feature, but one neat feature for both fun and for administration is the ability to mimic the physical movement of the mouse/the viewport of a given player. Ace of Spades did this, unofficially at first with a hack made by someone in the community, but it made it much easier to see aimbots due to their weird aiming patterns. Also, adding a through-walls outline of other mechs would enable an onlooker to see if a user might be using ESP hacks, since they would more than likely pre-aim before the mech became visible.
-
Game administration
-
Matches
- /match begin
-
/match pause + /pause (might be a nice feature!)
-
/match caplimit [cap_limit] (or cap rate or whatever it is)
-
/match logging [true/false] (whether to record a log file for each match, with detailed match stats)
-
Players
- /players [max_players]
- /spectators [max_spectators]
- /respawn [respawn_time]
-
/teambalance [number] (teambalance 0 turns off autobalancing, 1 means a difference of 1 player, etc)
-
/balance (shuffles players randomly into fair teams)
-
Maps (depending on how you're going to setup pub matches I guess)
- /map set [map_name]
-
/map cycles [num_cycles] (number of matches before changing to next map)
-
/map list [map_1] [map_2] ... (set the list of maps to loop through)
-
/progressivespawns [true/false] (default true, allow admins to prevent it)
-
Weapons (Soldat did this, don't know how good it'd be for AoT)
Basically, add the ability to restrict what is available in loadouts. Disable individual weapons/utilities/whatever.
-
Utilities
There have been suggestions to add ammo/health or something along those lines in terms of pickups or stations across the map. If this were implemented, some way of setting the amount you get from them and how often would be nice to be able to alter potentially, or remove them entirely.
That's all I can think of for now.