As said there are other factors here. Production cost being the primary one. Square-Enix spent a TON of money on developing Final Fantasy XIII and it's engine. The other games they made at the same time in order to pick up the slack to bring in money didn't really light up the charts. Dragon Quest from what I understand isn't touched by the Square side of Square-Enix either so they would be looked at as being in competition with each other. From my understanding this is why the Dragon Quest franchise hasn't been Sony based this generation. If the Square side had control of it it would be as the Square people are Sony first or Sony only in some cases. DQ is still handled by the Enix side. Between the two Dragon Quest IX clearly has to be the more profitable one. With the development of the other FF13 games I dare say that part of Square hasn't turned a profit yet.  At least looking from the outside that would be my conclusion.

If in the end Final Fantasy cost them far to much money and they don't bring in a significant enough profit I could easily see them changing how that series is handled int he future. The board of directors at Square-Enix would make that happen. The Square side wouldn't have much of an argument against that when Enix side has shown they can do tons in terms of sales for not even a fraction of the development cost. Overall if it wasn't for Dragon Quest I think Square-Enix might be in serious trouble financially.

Considering that DQIX is already ahead of FFXIII PS3 by 400K only shortly after Western release, this is a ridiculous statement. Is FFXIII supposed to sprout longer legs than is has managed already? Because that's the only way it would happen now. FFXIII is selling sub 15K worldwide weekly, DQXI steadily does half that every week in Japan alone, it wouldn't need much from the West to maintain a lead indefinitely.

On the other hand to outdo both versions combined and make up for the 1.1 million shortfall, it would have to have very strong legs in the West. Who knows if that's achievable.

Wait, FF13 sold only 5.7 million? On both HD consoles COMBINED?

... Just wow.

That is a very good point. I don't know much about the internal workings of Squre-Enix, but I do remember that the proposed merger between the two was delayed thanks mostly to the Spirits Within movie, where Enix became reluctant to merge with a Squaresoft who was, at the time, hemorrhaging a great deal of cash. 

If the Square side barely turns a profit this generation, Enix could very well consider splitting from the merger and going about it's own way.

Keep in mind, that FInal Fantasy XI has made more money than any Squaresoft, Enix or Square Enix Game Ever. If I recall the profit was around 100 million last year. That's with very little investment. And it's been making probably more than that since its release.

It simply is not as simple as what you said simple. For one. The engine they built for FFXIII, was crystal tools. Which is also being used in Square Enix Europes (Eidos) Deus Ex 3 game. Final Fantasy Versus XIII, FInal Fantasy XIV and probably other unknown games. So the cost of the engine =/= the cost of FFXIII
FFXIII has generated a net income of if you say $30 dollars a copy (I red somewhere the average for videogames is 32 or so) would result at around 170 million dolars.

Really both sides of it have a similar philosophy, make main games. and spam spin-offs/remaks

DQM, Dragon Quest Swords~ Crysis Core, FFX-2

In 8 Months. 5 in the West. Without any "International" release.

Just to provide a comparison...

Final Fantasy VII LT - 9.7M
Final Fantasy X LT - 7.95M 
Final Fantasy VIII LT - 7.86M
Final Fantasy XIII 8 Months* - 5.7M
Final Fantasy XII LT - 5.7M
Final Fantasy IX LT - 5.3M

It's doing a lot better than you make it sound.

Still it is kind of sad, that Dragon Quest is coming close to it. 

Blame Japan

In the West FF13 has almost done 4 Million, almost more than FF8 and it'll beat FF8 soon.

leaving just FF10 and 7 ahead of it.

Japan FF13 sales are shocking...first time FF did double in west than in Japan

_____

Edit:

http://www.vgchartz.com/worldtotals.php?name=final fantasy xiii

lol its done better in all regions than in Japan now. 

I wouldn't say it's sad at all really. I'd say it's great for Dragon Quest.

Final Fantasy XIV will bring in way more profit than any game for Square-Enix this generation

FFXI made $110 Million in 2009, like 6 years after its launch

Lets not forget Kingdom Heart and the FF games to be made with crystal tools which will have lower dev costs now.