No, I don't think they should remove the lockout. I've played SMN since 2.x and there are good reasons why they made that change. (For the record, 3.x was my favorite but I haven't tried out 4.1 yet.)
Previously, the decision of spending your Aetherflow in DWT was a calculated risk. Spending one gets your 30s timer rolling. Spending a second left you with a very narrow margin of error for refreshing with your last Aetherflow. For most players, this was actually a losing game. Don't believe me? Let's look at some numbers:
Using Fester in DWT was a potency gain of 20 (200 * .10).
Losing Deathflare was a loss of 440.
Losing 5 Ruin III upgrades was a loss of 660 ([200-80]*5*1.10).
It would take 55 ([440+660]/20) successful uses of Fester in DTW without dropping Aethertrail stacks later on to break even with dropping stacks just once. The number goes up if you add in Tri-Disaster/Contagion.
Even for reasonably good players, it was actually hard to come out ahead by cramming Festers into DWT in 3.x.
In 4.x, the Dev Team's stated goal was to lower the skill ceiling and raise the skill floor. Concurrent with the lockout, they also removed the 30s expiration of Aethertrail, which dramatically raised the floor. People seem to have forgotten how big of an issue dropped stacks were in 3.x.
The main issue with removing the lockout is how it would change the flow/rotation. Let us stop and think how the rotation would change: Spending Aetherflow on Fester in DWT would become the correct way to play SMN. Now that Ruin III is instant cast in DWT, Fester has a 5s cool down, and Aethertrail doesn't drop, it would be very easy to fit in all three Festers into DWT. There would be no tradeoffs or risks involved like there were in 3.x.
You might think that sounds great and are wondering why I am against it. Here's why: Aetherflow stacks give the SMN flexibility with burst DPS. Pigeon-holing SMNs into spending Aetherflow during DWT takes away that flexibility. Now that we can't burn extra mana to crank up the DPS with Ruin III, we don't really have anything else that affords us flexibility like that.
You might say, "if a phase is coming up where you need to burst, then you can just save your stacks." Now we are talking about raising the skill ceiling to where a SMN has to know what will happen in the next 60 seconds of a fight to plan their Aetherflow usage correctly.
"I just want the flexibility to refresh my Aetherflow if I'm late starting DWT." Taking into account the new meta of spending Aetherflow in DWT that would be created by removing the lockout, you would actually have the exact same amount of leeway in the rotation that we have currently.
Current: Refresh Aetherflow. 45s to spend and start DWT.
Proposed: Save DWT. Refresh Aetherflow. 45s to start DWT and spend Aetherflow in DWT.
Basically what this would do is change the rotation from "Spend Aetherflow > use DWT" to "Spend Aetherflow > save DWT until next Aetherflow is available." The current flow is what the Devs intended and I think it is better than what it would become if they removed the lockout.
For those situations where you are late in getting your DWT in, the opportunity cost of ending your DWT early with Deathflare has decreased dramatically in 4.1. You are no longer losing 5 Ruin III upgrades. You are only losing the 10% buff on 5 filler GCDs. Mathematically, it is now MUCH better to hit Deathflare early than to delay your Aetherflow and it's not that big of a DPS loss.
I try to base my opinions on real numbers whenever possible, so here's the math:
Tied to your Aetherflow are: 3 Festers, 1 Deathflare, and 1/2 Bahamut. Let's assume 11 Wyrm Waves with Bahamut. Keep in mind Bahamut's true potency is lower than advertised, which I will account for.
3 Festers: 600 = (3 x 200)
1 Deathflare: 440 = (400 *1.1 DWT bonus)
2 Akh Morns: 1046 = [(680 * 2)/1.3]
11 Wyrm Waves: 1354 = [(160 * 11)/1.3]
- Opportunity cost of 5 Garuda auto-attacks: 592 = [(110 * 7)/1.3]
Aetherflow Potency per second: 32.4/s = [(600+440)/60s + (1046+1354-592)/120s].
Ruin III potency gained in DWT: 13 = (130 * .10)
Ruin III in DWT potency gained per second: 5.2/s = (13 / 2.5s)
So if you delay Aetherflow to cast more Ruin IIIs in DWT, you are sacrificing 32.4/s to gain 5.2/s. In 4.0, the opportunity cost of losing Ruin III was much higher, at 26/s. [(150 * 1.1) - 100 = 65; (65/2.5s) = 26/s]. Ending DWT early for the sake of Aetherflow should not be the difficult decision it was in 4.0 because the DPS loss is now negligible.
TLDR: Lockout should not be removed. Removal would change SMN Rotation to save DWT until next Aetherflow is available. SMN would lose burst DPS flexibility because using Aetherflow outside DWT would be a DPS loss.
If Aetherflow cooldown is ready before DWT is finished, it is now better to use Deathflare quickly and refresh Aetherflow because of the Ruin/Ruin III changes in 4.1.