Most good 4x games I've played used economy as a deterrent to large forces.
If you place 'all of your units' to defeat the enemy's strongest base, you leave yourself opened for them to overtake all of your economic settlements. You do capture one planet, but end up losing 10-20. After a few turns, your opponent has managed to use these planets in such a way that their fleet is now larger than yours.
That's the best way to do it imo.
I'm perfectly fine with concentration of forces to force a victory, because, most times, this is a bad strategy in a good 4X game...
This penetration scenario could, unfortunately, be symmetrical: a very powerful "strongest base" that can challenge a great fleet means that the opponent is already open to large-scale invasion because other places are inadequately defended, exactly like the player. Enemy large fleets could be simultaneously ravaging the undefended interior of the other empire without necessarily meeting, possibly ending the game by randomly conquering the enemy capital.
Boring penetration and raiding with a single powerful force needs to be a worse strategy than more fun and challenging small battles of attrition and large-scale offensives of distributed small forces:the game should reward allocating the vast majority of ships to defense, so that "hunting parties" capable of conquering a planet are going to
- start small and grow slowly, as surplus ships are produced and places in the safe interior of the empire are demilitarized. Only an overwhelming economic lead (i.e. endgame cleanup) should allow building fleets from scratch instead of slowly reinforcing a large number of planetary defense forces and drafting ships from them when the risk is acceptable.
- struggle to keep pace with the growth of enemy forces. Too much defense is conservative and safe; too much offense should be a danger.
- meet their enemy counterparts, which should have a comparable strength, and be thinned out (even if they win) before they become stupidly strong.
This can be obtained through a combination of different means.
- Making ships slow enough, as the OP dislikes. What's important is avoiding fast long distance travel for strong fleets, so that they cannot defend the whole empire effectively; maybe short travels could be fast enough to not be annoying.
- Encouraging minor deep space battles in random contact locations along front lines, with planetary assaults as the result of a small (and not too quick) military campaign rather than as the standard type of battle. There is a fundamental difference between ships that are constantly located in some interesting place with a chance of being detected and intercepted and ships that effectively disappear when they start a trip and reappear at their destination thanks to the vast emptiness of space.
- Rewarding possession of planets etc. only after some time has passed, encouraging players to hold and defend locations rather than advancing and attempting to conquer objectives faster than they lose them elsewhere.
- Combat rules that reward slight superiority proportionally more than overwhelming superiority, e.g. guaranteed significant losses for the winner. For instance, splitting a fleet to fight two battles with a 2:1 ratio could be better than fighting one battle with a 4:1 ratio and the other with the survivors of the first (maybe because there is a necessary delay allowing the enemy to send reinforcements).