Well... I am not business expert but it's a tradeoff.
Crappy MODO ALREADY grosses them $X/month (maybe $100,000?), and costs some amount below that to maintain. Let's say 2-3 FTE which is about $500K/year. The hardware is probably 1/10th that, so forget it.
Replacing it with new software is going to cost at least several million over 2-3 years - maybe as much as $50M total (online videogames are expensive to develop) , and it has to be paid upfront. And you still have the same maintenance costs. So, in order for this to be a good investment for WOTC/Hasbro they have to be sure to recoup their investment by increasing the number of subscribers/players that pay.
You have to also consider the backlash if they "upgrade" and it bombs. (i.e, forums, obamacare).
Free versions or competitors probably cannot compete for serious MTGO players because their won't be the gambling/payoff aspect of it. And MTG is still the biggest and best CCG game around, and the online game synergies with the paper one.
On the postitive side, eventually technology will badly outstrip their software and they will have to replace it. They probably are already working on a new version, but maybe it's only a couple engineers with prototypes.
I think $100,000 per month is a gross understatement.
The modo PTQ alone had over 700 people which is over $28,000 for a singular event. In addition to high profile events like this, drafts consistently fire at all times.
I think I read somewhere that MTGO does not reach the sales of paper equivalent but it is significant enough to where if MTGO just ceased to be, WotC would be losing out on a lot of money. They have enough money to be able to make it better, they just haven't, because people have seen it as "good enough" to get by. I think this was the straw that broke the camel's back and that something is going to be done now.
The upgrade leading to more problems argument is a bit near sighted if you ask me. Doing nothing to a system that is broken will not fix the system.