The fuel collection system was something implemented a long time ago, though we have made a more recent alteration to the energy efficiency of ships.
The reason why fuel collectors were added was simply to reduce the reliance of refueling at bases. Sometimes, we operate in systems which have no bases what-so-ever, so without them we would have to wait for quite a long time to refuel the ship so that it is combat capable. Rather than having to hop from base to base in our home systems too, we could just refuel when needed where we were. In protracted combats, it created interesting situations in which a “fallback” or recovery location could be designated (though this hasn’t been something we’ve looked in depth) and ships attack, then retreat to recover, whilst the next ship attacks. We have done it when escorting ships, with one ship recovering/ providing escort whilst the others attack.
More recently, we modified the energy efficiency of ships. The intention was to change the focus from power being consumed by warp and impulse, and shift it to the weapon systems. It meant we could travel at Warp 2 as standard and still maintain a decent energy level. Now we are freer to use higher warp factors like warp 3 and 4 without finding we have 0 energy after crossing only a sector or two. Of course, in combat using the weapon systems, energy starts to drop more rapidly. Activating shields and firing primary beams consumes energy at a much more rapid rate now.
All these actually change engineering, and not in a way that detracts from the role. Instead of watching the energy levels and having to conserve constantly, you can boost energy. You have to be more aware at when the ship is in combat though, as that is when energy will start to drop. The difference is, you now have to carefully manage heat and decide where your coolant is going to go as you can easily boost multiple systems at a time and keep them at high levels. Previously, a ship sitting at 100% energy on all systems would gradually run out. Now it will slowly recharge the energy instead. Boost several systems up and enter combat, and you have both energy and coolant to manage. The ship will be maneuvering more and be in combats longer, away from bases. We are more reliant then ever on engineers getting the most from the ship, handling the damage and keeping the ship running at peak performance.
The engineering game is now much more about getting the ship to perform at peak performance all the time, rather than playing conservative and squeezing system to try and make them efficient.
One final thing: another knock on impact is on the homing torpedoes. They are no longer glorified batteries, but usable and effective ordnance weapons.
Hope that all makes sense!