I've never tried to build anything with that many traces as separate subplots but I don't see why you couldn't have the same resolution if you set the axes limits the same as the individual axes limits in the stackedplot -- they're essentially the same thing excepting the subplot creates a figure which contains axes with space for labels and all like miniature figures instead of just more bare axes.
y=randi([-50 50],1000,2); % just some random data
figure
hSP=stackedplot(y); % example stacked plot to see how big is...
SPposn=hSP.Position; %
% examination shows [Left Bottom Width ...] same for stacked plot axes both subplot axes
% within the overall position. Height is what is different -- the sum of heights subplots
% < height of same number of lines in stacked plot cuz don't leave room for the axes
% as subplot() does...
figure
for i=1:2, hAx(i)=subplot(2,1,i); end % and two subplots to test the idea
AXposn=reshape([hAx.Position],4,[]).'; % the position vectors for each subplot (top to bottom)
dHt=SPposn(:,4)-sum(AXposn(:,4)); % the differential total height between to figures
AXposn(:,4)=AXposn(:,4)+dHt/2; % split the difference and add to subplot heights
AXposn(1,2)=AXposn(1,2)-dHt/2; % lower the bottom of top to make up for added height
hAx(1).Position=AXposn(1,:); % set each subplot to new position...
hAx(2).Position=AXposn(2,:); % top grows down, bottom grows up
hXAx=get(hAx,'XAxis'); % get the XAxis numeric ruler handles
cellfun(@(hNR) set(hNR,'Visible','off'),hXAx) % turn x axis off
% now ready to plot into adjusted axes...altho could plot first, then adjust position.
axes(hAx(1)) % first suplot
hold on % keep plot from mucking on what we've done
plot(y(:,1)) % same data to compare visual
axes(hAx(2)) % ditto same for lower subplot...
hold on
plot(y(:,2))
Result is that actually have slightly more space in the subplot(() it appears than in stacked plot --there's still a little background between the two plots there and none betwee two subplots. Apparently stackedplot() uses an internal shrinkage factor on actual individual axes it creates within the overall larger container axis. I didn't try that refinement here...but a "roll your own" wouldn't be too hard to put together for specific purpose if don't try to make it handle all the bells and whistles.
