I know I'm late to the game on this topic and Trouble is probably gone. But, it's just like everything in this game. As you progress things cost more. As you move up the Discovery chain, the discoveries cost more resources for each discovery and each level within a discovery. As you level up your production buildings, they cost more resources.
As you level up discoveries you get more powerful units. As you level up buildings you get more capacity and production. As you level up Prestige you get more benefits, as shown above.
You don't have to buy Prestige activators or level up discoveries or level up buildings. You need to, or get to, decide if the benefits are worth the cost. It's your game. For me, the benefits of Prestige activators at level 9 and 10 are worth the extra rubies. It's a bonus if you can buy them at a discount.
Fair seas to all.