^To be fair now, Sub Terra fits into the marketing extremely well, just took some months to get it to that level...
Now Mouse I'm not fully defending Merlin for some of their implementations at Alton (since that's really the only park that's seen these things, the others have barely had anything that would affect them to a large enough degree to warrant bothering about), but they've not (to my knowledge) had anything to do with the public transport options? Dunno why that's been brought up...
But let's look at some of the issues the park will encounter:
Increased cost of running the park due to new attractions
This will naturally be an issue with all parks, but perhaps is part of the reason the cost of entry and other things are so high these days... Indeed, look at the food quality these days, perhaps to get this higher level of quality (in comparison to former in house food) a higher cost is required?
Then of course with new rides, the park needs more staff (and Sub Terra is a strange concept from the park, as it requires so many) who of course all need paying and add to the wage bill... Again, easiest method would be to increase entry prices... It's not the park's fault that investment into the park actually requires them to expand the budget a lot more in the long term, and indeed, to help increase costs, as the rides get older, maintenance bills go up, so really it's a sharp edge the parks already tred regarding money that NEEDS to be spent to even exist, let alone the extras...
The locals
Just gonna plug this in one really, we all know that the locals and Towers have a very love/hate relationship, and perhaps this is a reason for a lack of late hours (as well as operating costs) we see in the summer... It's all well and good saying that the park should open till 8/9/10 during the summer, but due to the local roads and the locals themselves, perhaps this cannot actually be implemented because of the backlash the park would face? Granted they might (big might here, as the parks might not be instantly successful with late hours here) make money back due to people eating a second meal, but it's not just the guests on park Towers have to please, but the locals as well (see also why Chessie never shut later than 8 before now, hell Vampire even has a dedicated bedtime due to Monkey Puzzle)...
There are other factors affecting the lack of attendance out of the control of Merlin
As mentioned, this has really been a bad year for the parks in general, BUT, why is this? This year is completely unique so far due to not only the events, but also the weather being ridiculously messed up in what usually are busier days for the park... It's amazing how much heavy rain will stop the general public not bothering to venture outside really, and considering how bad it was last month, well...
Then the Jubilee and the Olympics... London is dead, and as such, this factor has spread to the tourist attractions, indeed, it's probably right now the best time of year to visit (DO IT, GO NOW!) but there is that thought from everyone that because it's summer, because of the olympics, these places will be busy... This mind set I doubt will ever change, and as such, ALL the parks (aside from maybe Lego) as suffering to a relatively heavy degree...
Indeed, it COULD be considered that maybe someone saw this and as such took the precautions early on to help the park withstand an awful year? It's not particularly that far-fetched that someone would have thought that, especially at Towers... The London parks were probably waiting for the crowds with open arms, whilst Towers are in that awkward position of being out of the way and trying to compete with the cheap trips abroad for Londoners...
What's the betting that next year it all goes back to normal and we all forget about this? Especially as Towers and Chessie are both getting major rides next year, which will certainly entice people to return to the parks...
It could be a lot worse anyways (it's not always shiny under the independently owned banner, and it's arguable that Merlin APs are better value than other parks versions), but Merlin themselves set the fall up, what with the whole "compete with Disney the financial juggernaught that they are" crap they began with, when really, they should've just gone for their own thing...
They keep investing in more Midway attractions which is interesting, as they are the most profitable places in the portfolio... Perhaps more of these will allow for more money to be invested back into the
parks in the future?
TL;DR - There are lots of factors which will affect the decisions, and since it's been a really bad year for the park as a business, is it really surprising they're trying to get money to ensure profitability?
