There most definitely are certain merits to such games - and their simplicity yet obvious popularity show that there is a definitive interest in the design.
Though to reward "souls" exclusively in "gems" may well be the wrong approach.
For starters, its a matter of perspective. Gems are still seen as the freemium cash currency, its that stigma, even more so than their role (since the role is still that of cash-currency, a quick cheat to advance) that is damaging the game from the perspective of PC players.
The initial step in that direction would be to rethink the role that gems represent.
Since the "gems" in their new format would represent the souls of your previous world/incarnation, calling them gems is silly.
Instead a form of divine energy or sacrificial energy would be more apt. It would be fitting within the confines of the game.
Moreover, since (especially from a PC perspective) this currency does indeed come through the sacrifice of your people.
Both through the Pit of Doom aswell as through this 'incarnate system' - and potentially through other means to be implemented in the future (I could forsee less 'evil'-connotated forms of sacrifice like Priest-styled followers that sacrifice their lives to the devotion and worship of their god.
Or even the sacrifice of material wealth and goods or even animals, as opposed to the sacrifice of people.
Sacrifice can take many shapes and forms.
On top of that, there should be an overarching line to represent your Godhood in all of this.
A sustained currency is one thing. But you should also grow in stature as a god.
Obtaining new powers or strengthening old ones. Learning new ways of dealing with things, but also encountering new obstacles as older ones become inconsequential.
Perhaps with the growth of your power and through the repeated sacrifice/renewal of worlds, some of that energy leeches out and forms minor deities or other evils.
And perhaps some of the people that were 'sacrificed' in the reincarnation did not share your views and in "resetting" the world they created a new god that now opposes you.
As
Deth says, it is also quite essential if this path were taken, that procedurally generated worlds and natural exploration becomes a thing.
Now I don't know how that would fit in (or even could fit in) with the rest of the current design.
Though I suspect that such a drastic overhaul and change of direction may well prove problematic.
Some key elements though, these new worlds could blow some life back into the old concept of a Jupitersized world.
Only instead of "one world" its many worlds that have a combined surface area the size of Jupiter (a shift in focus perhaps due to technical constraints).
Similarly it would allow the return of other concepts such as a living, breathing world - since the worlds would have a different focus and scope than they would have if you are working from a pre-made map and a linear style of play.
Not to mention ofcourse that the ability to reset or even tend multiple worlds, would allow you to deal with the growing population posing pathfinding issues.
It would allow for the creative solutions to a number of problems currently posing the game - at the cost of having to redesign some of the core concepts.
Perhaps one of the big questions would be, how do you 'retain' some of the progression of your people - or alternately speed their progression through the ages up allowing you to get further and further along on each incarnation.
It would most definitely allow for a much longer replay value than the current linear 'pre-made' format does, which would fall in line with Peter's idea of having the game be played for years to come.
All in all, there's a lot of questions and unknown variables.
And while I believe there may be merit in the idea as a whole, I'm not sure whether it would be suitable for Godus as Peter sees it.
So we would need to hear his view (and that of the design team) to even consider taking this seriously within the confines of Godus.
There's potential, but its a drastic shift.
*EDIT*
One small addition - I've looked at Clicker Heroes myself and I'm aware of other 'clicker' games.
And while there are inherent values to the mechanics.
Ultimately these aren't necessarily games that you "play" as much as they are activities that you tend to.
Much like the mobile games like Clash of Clans or Candy Crush - its something that you load up on a break, click through then let run either idly in the background, let tick by its default offline calculations or if you're really invested use an auto-clicker to "speed it up" so to speak.
So there are definite pitfalls in bringing these concepts to a PC game, where you can't just load it up in a matter of seconds, play for 5 minutes and then be done.
PC's and PC games just aren't suitable for that kind of play-style currently. Atleast, not for the expectations and purposes of many PC gamers.
