Yes your right, it is more expensive to install the last 10,000 seats than the first, it also even more expensive to add the those additional seats later down the line. Which I believe they will have to do at some point, the fan base will only ever grow and need for additional seats becomes greater.As others have mentioned, a lot of it will have come down to the economics of it... The cost to install the final 10,000 seats is greater than the cost to install the first 10,000, but they will also be sold cheaper as they'll be further away from the pitch... So the numbers don't stack up.
The average attendance at Goodison last season was around 39000. If we (and I'm sure we will) sell out the new ground every week, you're talking an average attendance of maybe 51000 (got to assume away fans won't sell out every week). That's a 12000 jump, or a 30% increase on GP. These are significant numbers.
The stadium is for the next 100-150 years, 52,000 is simply not enough. Future expansion is certain.