Everybody grows a beard
EDIT>>In the interest of adding something useful as indicated by the next post
1) Proper starfighters and bombers with dedicated carriers
2) Refit some of the TNG era ships with Defiant or Special Voyager style armor, don't go crazy just add it over critical areas sorta like a tank with applique armor
3) Don't build your ships with long necks and warp engines on thin pylons
4) Add cloaks, might ruffle some treaty stipulations but hey, for war not for peace
5) Always have your ships operate in BattleGroups of some kind, no farting around space by your lonesome
6) Add dedicated ships for escorting your heavies, torpedo frigates, phaser cruisers ect. granted they might die quicker but they add more distractions
7) Ditch pretty windows, add more armor plate to new ships
8) Don't leave the bridge in a exposed position were anybody can shoot at it
9) Improve your ECM capabilities, jamming coms, sensors ect
10) Clone Kirk
2nd EDIT>> I have been informed by more knowledgeable parties that they should in fact grow goatees:
