Big fleets are fun, and will still be quite possible, indeed probable.
However, what the upkeep and economic model will mean is that you can't just rely on many large flees, you as have to earn and upkeep them. This contributes to the new valuing of each individual asset as well as groups, making each fleet and its contents more important and widening the spectrum in terms of the kind of battles going on (from skirmishes to epic clashes) and also thus increasing the player's requirement to properly manage both their fleets and economy.
Furthermore, the potential galactic population limit will be much higher; however you'll need to be wise and have some economic prowess to make use of it. Another trade-off.
It's a part of the wider game experience in which one has to act as a galactic strategist instead of just someone throwing endless supplies of ships at things.
From a dev's point of view, it also tweaks the balancing slightly; whilst losing ships means you have major strategic issues with defence and obviously losing territory, the financial repercussions reflect a more accurate war economy - you'll need to invest to reinforce your numbers, but the loss of the vessels will reduce your maintenance overhead.