How many companions should be able to follow your Dovahkiin at one time?
2-3 well done companions who has unique characters and personalities, decent quest lines, have different skills, react on events, companions like
Companion Vilja
http://www.tesnexus.com/downloads/file.php?id=28977
Ruined Tails Tale
http://www.tesnexus.com/downloads/file.php?id=3027
or
Julan, Ashlander Companion 1.3
http://lovkullen.net/Emma/Kateri.htm
And support of not so complex done mercenaries from Fighter guild, ability use ranks in guilds to command certain guild members, or ability permanent summon in cost lowering maximum of Magicka some daedra servants, or creating an undead servants from corpses, such companions can be done in larger numbers and have simple abilities and functions
Should you be able to customize the script/strategy of each companion?
Yes, but a little more complicated (i.e. heal me if i go below 50% health , or Run away and hide if you go below 50% health)
Such scripted rules isn't hard to be done and as template they can work for most companions
Should you be able to utilize the companion's skills? (i.e. having your rouge pick a lock or having your mage cast waterwalking on the party)
Definitely yes since thats expand variability in game and player can concentrate on different ways of building own character.