I do not like the increasing cost of spies, which leads to the leader of the board effectively being unable to defend against spy attacks. This was discussed in other threads, already, so I won't go into detail.
I am looking forward to the new system, but I would really approve for a system where you could train offensive and defensive spies, the latter with only modestly rising costs.
There's a wonderful building that will take care of that issue for you. A bit on the expensive side, but then so are spies, aren't they

CE buildings will keep spies off your important worlds, and the AI tends to go after stock exchanges anyway - you may as well leave those spies in place late-game, as removing them costs more than what you're losing to the disabled stock exchange.
As for the rising cost of spies, it's an absolute necessity. Otherwise, if spies are fixed in price, they will be unobtainably expensive early in the game, go through an reasonably affordable phase midgame, then become dirt cheap late game, to the point where you may get several per turn. You might make an argument for adjusting how fast the cost grows, but growth is necessary.
I like the idea of offensive vs defensive spies, but even better would be a passive counter-espionage tech line. Each tech may give a 5% chance of passively removing a spy each turn, up to a maximum of maybe 20%. Have the counter espionage building available after the third or fourth tech, and still allow spies to be used defensively when necessary. (Sure, the passive tech would remove the spy from your 700% bonus industrial sector
eventually, but who would really want to wait?)