Because they are further down the tech tree and you can use them for attack and defence also you don't have spend resources on it and can build bireme with Trieme for a stronger fleet
yes but you understand that
1) Triremes are generally garbage and are only useful in hotly contested frontline cities as you can back and frontsnipe with them(CQ Only), other than that they're pretty useless
2) The resource/time favor trade off for gaining 1 single trireme is nothing compared to the ability to cut the training time of any ship you want in half.
here I did the math:
Assume all training times for current system have 30 harbor and COTO running. No heroes, rituals, tokens, or grand armings were included.
Optimized Trireme nuke with suggested system:250 Tris= 15,000 favor 0 Resources (drawing favor gen from my wonders optimized builds with a 50% favor token running 220 favor per hour) that would take about 68 hours to get a full trireme nuke.
Optimized Trireme nuke with current system: 450,000 wood 292,500 rock and silver. Training time: 53 Hours.
Optimized LS nuke with current system: 400 LS=468,000 wood 108,000 stone 288,000 silver. Training time:53 hours
Optimized Bir nuke(which most people don't have but lets do the calculations anyways):500 Birs= 360,000 wood 315,000 stone 81,000 silver. Training Time:45 hours
Bottom line: It's way more efficient to have the current system as favor is much harder to get than res especially once you start to grow in cities. The idea that the tech tree is limiting in any way is irrelevant as most people will level the academy to 34(then in an optimized nuke like the ones above: demolish) anyways. The only reason that the system you're proposing even looks close to the other ones is because I'm basing the favor calculations on a world where I have over 200 cities most of which are built for wonders(max temples, divine statues in some places merchants in others) in a speed 4 world. If we half my production and keep the 50% favor token on it takes 136 hours, at which point you could train two trireme nukes, 2 LS nukes, and 3 Bir nukes. Basically this is just a terrible idea.