1 line with many ports or many lines with 1 port equates to the same.
Remember CLI can look tidy to us but behind the scenes the router still has to do the same lookup on a packet for that port.. so the ACL method does not really matter.
On PIX/ASA you can do turboACL which compiles the ACL in binary to speed lookups up (meant for huge ACLs though (thousands of lines).
Even object groups on PIX/ASA are just to make life easy on CLI, still a lookup on each port.
So in summary, nothing you can do.. If the ACL's keep growing and as CPU average gets higher maybe we need to look at getting proper firewalls (ASA) in to do the firewall function.
Router IOS firewall throughput is lower than a proper firewall.