The choice between the SH and the F-35 comes down largely to what kind of war Canada wants to be able to fight.
The F/A-18E/F has serious performance issues (right across the board), but has a lot of gas, can carry a lot of bombs, and is pretty cheap (at today's fuel prices, maybe not so much in a few years). It was essentially tailor-made for the kind of mid- to low-intensity, negligible air threat, limited scope, coalition conflicts we've seen since the end of the cold war. It's not so much a fighter anymore, but it is one of the better bang-for-your-buck bomb trucks out there. It's range/payload/hardpoint combination means in a low-threat environment it will be able to hit way more targets per sortie (although potentially at a lower sortie rate, given it's barely tolerable cruise speeds)
It also has excellent growth potential for future avionics, and is already carrying (in some capacity or another) all of the major systems a 5th gen fighter needs (Phased Array radar, ATFLIR pod, JHMCS, Link 16, etc), despite most definitely being a 4th gen aircraft (more akin to the Gripen and Flanker than Rafale or F-22).
The F-35 is a bit of an unknown, but the technology demonstrators have already shown they have excellent performance potential, especially since their version of the F119 is expected to be rated at 44,000lbs of static thrust once it hits production.
It's avionics suite is going to be more mature (with a large portion of the architecture based on the F-22A's) than many critics claim, although I'm 100% certain that customers will be waiting years after delivery to get the software for basic capabilities that it's supposed to have out of the box.
But the F-35 is most definitely designed with high-intensity conflict in mind. The large emphasis on stealth, EW (yes, stealth is a part of EW, I know), and supercruise are all indicators that this aircraft means business.
There is really only one deciding question between the two:
Does *Canada* mean business?
Having spent my entire life under the Cretien dynasty, I can say uncategorically that the answer has been NO.
But how long this will remain the case? We are looking at a procurement that will be here for decades.
If we are willing to relegate the CF to being an add-on formation to whatever major power is doing the fighting, then the Super Hornet is definitely the way to go. The next time a massive multi-national coalition starts bombing a vastly-outnumbered and technologically hopeless tin-pot dictator, we can toss in an extra half-squadron to show solidarity, and it won't cost us too much money.
But if the CF gets stuck fighting a modern opponent with only the UK or perhaps a small European coalition at our back, with no USN/USAF to kick the door down for us, we will be in trouble. IMHO, the Super Hornet is not up to the kind of air superiority or high-threat SEAD tasking that a modern high-intensity war is going to demand.
The F-35 is more expensive, probably MUCH more expensive by the time it hits production (although the Canadian government has already dumped more than $400 million into the program to join the Tier III group, and to fund companies bidding on R&D and production contracts).
But it's a full generation newer, and will be able to fill the SEAD and air superiority roles with the best of them, as well as providing bomb-truck services (just not quite as efficiently as a SH).
So:
Spend as little money as possible (the SH really *is* the cheapest feasible option), have new fighters now, but relegate the CF fighter squadrons to being the Canadian Wing of the USANG
Or fork over several hundred million dollars more, and have one of the major tools that will be ESASENTIAL for high-tech expeditionary warfare in the future. Remembering that this is money which will be completely wasted if we don't have some of the other tools (or at least access to them), or the POLITICAL WILL TO USE THEM. The last one being the most important.
Are we content only being able to go to war with America's active support?
Even if we provide the military with the tools they need to go to war, will the Canadian government/public have the stones to send them when they are needed?
I think the F-35 is easily the best way to go for a Hornet replacement. Right across the board. But my pessimism leads me to say that the Canadian public and government don't have the stomach for any kind of conflict with anyone who can fight back.
Pragmatically, I can say that the SH will probably suffice. But I would rather see F-35s with maple leaf roundels just in case things head south some time in the next 40 years or so (we're talking about preparing for contingencies that may arise when our children/grandchildren are in uniform).