The whole notion of moving these cultural and historical institutions due to some perceived issue of accessibility strikes me as ludicrous. The Science Centre is not about to pull up stakes and move downtown just because a handful of people on UT feel it's inappropriately located. It's fine where it is. If it needs work, it'll either secure the funding or it will die off. Moving it would be hideously expensive and would still amount to a needless roll of the dice.
As for the Brickworks, it's where it is because it's the site of a former brickworks, a historical industry which created many of the bricks which have long upheld the rooftops over many a Torontonian noggin. The whole reason you visit it is to get a half-way authentic sense of what Toronto was, decades ago. Too, its newfound life as a tourist destination and vibrant people place has a great deal to do with it being situated in the Don Valley - a place of natural beauty. Great place to take the kids, walk the dog... and the market, though pricey, has some excellent foodie attractions.
By contrast, there's not a whole lot of places left in downtown Toronto to accommodate every museum and tourist attraction one can imagine - especially not along the high-value lakeshore area.
Moving everything downtown in order to make some kind of greater impact just seems desperate and ill-conceived.
If a museum or other kind of science and cultural institution is deemed publicly desirable, people will find a way to get themselves to it, period. The transit situation is a moving target, too - the city is bound to be far better serviced by public transit in ten year's time. That had better be the case, or we are well and truly screwed.
And if you want to visit the brickworks, you are not limited the car. There are these cool things called bikes and - even more amazing - they have their own dedicated pathways taking you to and from the Brickworks. You really have to see it to believe it, but it works.
Bringing it all back to Ontario Place: - since it's really gone downhill, it's a bit of a crapshoot to predict that sheer lingering nostalgia for its glory days will ensure that it'll be revitalized and restored. More likely, perhaps, is the possibility of the old site being subsumed into some larger, different entity. As it stands, it's been in the dumps for ages now. People have a nasty habit of forgetting once-vibrant city destinations once they've been permitted to go to seed.