As mentioned, keeping a reserve is standard for warfare. If it is early in the game and you have no strategic depth, of course the first major fleet battle may decide things. That's part of the hazard of early warfare. If things are later on and you're foolish enough to lose your entire fleet in one cataclysmic event, then a) you should have time to rebuild at least something, b) you should have done better reconnaissance and discovered what your enemy was using and c) even if you lose a war, you're unlikely to lose more than a few planets, which could be made up through colonisation and war elsewhere. In addition, your enemy's conquests will alarm neighbours, which gives you opportunities to make alliances. You also have the advantage of a five year break, during which you can build a fleet tailor made to destroy the ships that trounced you the first time round! I saw lots of things to make life difficult for the conquerors and give the losing side time to recover.
It is important that conquest and expansion isn't made too painful. Otherwise, why would anyone ever declare war? A game where all the mighty war fleets stay at home staring across the border intimidatingly can be tense; cold wars are often fun to simulate. But if no one dares actually start the main event, that will eventually grow boring!
